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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 14A

Proxy Statement Pursuant to Section 14(a) of the
Securities Exchange Act of 1934
(Amendment No. )

	Filed by the Registrant			☒
	Filed by a party other than the Registrant			☐

Check the appropriate box:

☐

Preliminary Proxy Statement

☐

Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))

☒

Definitive Proxy Statement

☐

Definitive Additional Materials

☐

Soliciting Material under § 240.14a-12

ALTO NEUROSCIENCE, INC.

(Name of Registrant as Specified In Its Charter)

(Name of Person(s) Filing Proxy Statement, if other than the Registrant)

Payment of Filing Fee (Check all boxes that apply):

☒

No fee required

☐

Fee paid previously with preliminary materials

☐

Fee computed on table in exhibit required by Item 25(b) per Exchange Act Rules 14a-6(i)(1) and 0-11

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ALTO NEUROSCIENCE, INC.
650 Castro Street, Suite 450
Mountain View, California 94041

NOTICE OF ANNUAL MEETING OF STOCKHOLDERS
To Be Held On May 12, 2026

Dear Alto Neuroscience, Inc. Stockholder:

You are cordially invited to attend the 2026 annual meeting of stockholders (the “Annual Meeting”) of Alto Neuroscience, Inc., a Delaware corporation (“we” or “us,” or the “Company”), which will be held on Tuesday, May 12, 2026 at 8:30 a.m. Eastern Time. The Annual Meeting will be virtual, held via live webcast, through which you can listen to the meeting, submit questions, and vote online. There is no physical location for the Annual Meeting.

The Annual Meeting will be held for the following purposes:

To elect the Board of Director’s two nominees named in the accompanying proxy statement (“Proxy Statement”) to serve as Class II directors until the 2029 Annual Meeting of Stockholders;

To ratify the Audit Committee of the Company’s Board of Directors’ selection of Deloitte & Touche LLP (“Deloitte”) as our independent registered public accounting firm for the fiscal year ending December 31, 2026;

To approve an amendment and restatement of our 2024 Equity Incentive Plan (the “2024 Plan”) to treat outstanding pre-funded warrants the same as outstanding shares of Common Stock for purposes of calculating the number of shares to be automatically added to the share reserve thereunder pursuant to the “evergreen” feature of the 2024 Plan;

To approve an amendment and restatement of our 2024 Employee Stock Purchase Plan (the “2024 ESPP”) to treat outstanding pre-funded warrants the same as outstanding shares of Common Stock for purposes of calculating the number of shares to be automatically added to the share reserve thereunder pursuant to the “evergreen” feature of the 2024 ESPP; and

To conduct any other business properly brought before the Annual Meeting.

These items of business are more fully described in the Proxy Statement accompanying this Notice.

The Annual Meeting can be attended by visiting www.virtualshareholdermeeting.com/ANRO2026 and entering your 16-digit Control Number included in your Notice of Internet Availability of Proxy Materials, proxy card or voting instruction form sent to you. You may log-in to the Annual Meeting beginning at 8:15 a.m. Eastern Time, on Tuesday, May 12, 2026. Please refer to the additional logistical details and recommendations in the accompanying Proxy Statement.

The record date for the Annual Meeting is March 16, 2026. Only stockholders of record at the close of business on that date are entitled to notice and may vote at the Annual Meeting, or any adjournment or postponement thereof. A stockholder entitled to attend and vote at the Annual Meeting is entitled to appoint one or more proxies to attend and vote instead of him or her at the Annual Meeting, using the proxy card provided or using an electronic proxy card by telephone or via the internet in the manner described in the Proxy Statement. A proxy need not be a stockholder of record.

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		Important Notice Regarding the Availability of Proxy Materials for the Annual Meeting of Stockholders to be held on May 12, 2026, at 8:30 a.m. Eastern Time via live webcast.
		This Notice, the accompanying Proxy Statement and our 2025 Annual Report on Form 10-K are available at www.proxyvote.com. Your vote is important. Whether or not you plan to attend the Annual Meeting, we urge you to submit your vote in advance via the internet, telephone or mail.

By Order of the Board of Directors

Erin R. McQuade
General Counsel and Chief Administrative Officer; Corporate Secretary

City of Mountain View, California
March 26, 2026

You are cordially invited to attend our Annual Meeting via our virtual meeting platform. Whether or not you expect to attend the meeting, please vote over the telephone or the internet prior to the Annual Meeting as instructed in these materials, or if you receive a paper proxy card by mail, by completing and returning such proxy card promptly in order to ensure your representation at the Annual Meeting. Even if you have voted by proxy, you may still vote at the Annual Meeting.

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ALTO NEUROSCIENCE, INC.
650 Castro Street, Suite 450
Mountain View, California 94041

PROXY STATEMENT
FOR THE 2026 ANNUAL MEETING OF STOCKHOLDERS

May 12, 2026

MEETING AGENDA

Proposals	Page	Voting Standard	Board Recommendation
Election of Directors	8	Plurality of the votes of the shares present or represented by proxy and entitled to vote in the election of directors. Only votes “For” will affect the outcome of the vote; “withhold” votes and broker non-votes will have no effect on the outcome of the vote.	“For” the director nominees
Ratification of the selection of Deloitte & Touche LLP as the Company’s independent registered public accounting firm for fiscal year 2026	20	Affirmative vote of a majority of the votes cast on this matter, voting affirmatively or negatively (excluding abstentions and broker non-votes).	“For”
Approval of an amendment and restatement of the Company’s 2024 Equity Incentive Plan to treat outstanding pre-funded warrants the same as outstanding shares of Common Stock for purposes of calculating the number of shares to be automatically added to the share reserve thereunder pursuant to the “evergreen” feature of the 2024 Equity Incentive Plan	22	Affirmative vote of a majority of the votes cast on this matter, voting affirmatively or negatively (excluding abstentions and broker non-votes).	“For”
Approval of an amendment and restatement of the Company’s 2024 Employee Stock Purchase Plan to treat outstanding pre-funded warrants the same as outstanding shares of Common Stock for purposes of calculating the number of shares to be automatically added to the share reserve thereunder pursuant to the “evergreen” feature of the 2024 Employee Stock Purchase Plan	30	Affirmative vote of a majority of the votes cast on this matter, voting affirmatively or negatively (excluding abstentions and broker non-votes).	“For”

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	QUESTIONS AND ANSWERS ABOUT THESE PROXY MATERIALS AND VOTING					1
	PROPOSAL 1 ELECTION OF DIRECTORS					8
	BOARD OF DIRECTORS AND CORPORATE GOVERNANCE					11
	Independence of the Board of Directors					11
	Board Leadership Structure					11
	Director Commitments					11
	Role of the Board of Directors in Risk Oversight					11
	Meetings of the Board of Directors					12
	Information Regarding Committees of the Board of Directors					12
	Board Membership Criteria					15
	Non-Employee Director Compensation					16
	Stockholder Communications with the Board of Directors					18
	Code of Business Conduct and Ethics					19
	Insider Trading Policy					19
	Corporate Governance Guidelines					19
	Hedging and Pledging Policy					19
	Equity Award Grant Policies and Procedures					19
	PROPOSAL 2 RATIFICATION OF SELECTION OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM					20
	Principal Accountant Fees and Services					20
	Pre-Approval Policies and Procedures					21
	PROPOSAL 3 APPROVAL OF AMENDMENT AND RESTATEMENT OF THE 2024 EQUITY INCENTIVE PLAN					22
	PROPOSAL 4 APPROVAL OF AMENDMENT AND RESTATEMENT OF THE 2024 EMPLOYEE STOCK PURCHASE PLAN					30
	EXECUTIVE OFFICERS					34
	SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT					35
	EXECUTIVE COMPENSATION					38
	Summary Compensation Table					38
	Narrative to the Summary Compensation Table					39
	Outstanding Equity Awards at Fiscal Year End					40
	Employment Arrangements					41
	Potential Payments Upon Termination or Change in Control					42
	Other Compensation and Benefits					43
	401(k) Plan					43
	Compensation Recovery (“Clawback”) Policy					43
	Limitation of Liability and Indemnification					43
	Emerging Growth Company Status					44
	SECURITIES AUTHORIZED FOR ISSUANCE UNDER EQUITY COMPENSATION PLANS					45
	TRANSACTIONS WITH RELATED PERSONS AND INDEMNIFICATION					46
	Policies and Procedures for Transactions with Related Persons					46
	Certain Related Person Transactions and Indemnification					47

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	HOUSEHOLDING OF PROXY MATERIALS					49
	OTHER MATTERS					50
	APPENDIX A—AMENDED AND RESTATED 2024 EQUITY INCENTIVE PLAN					A-1
	APPENDIX B—AMENDED AND RESTATED 2024 EMPLOYEE STOCK PURCHASE PLAN					B-1

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QUESTIONS AND ANSWERS ABOUT THESE PROXY MATERIALS AND VOTING

Why did I receive a notice regarding the availability of proxy materials on the internet?

Pursuant to rules adopted by the Securities and Exchange Commission (the “SEC”), we have elected to provide access to our proxy materials over the internet. Accordingly, we have sent you a Notice of Internet Availability of Proxy Materials (the “Notice”) because the Board of Directors (the “Board”) of Alto Neuroscience, Inc. (sometimes referred to as “we”, “us”, the “Company” or “Alto”) is soliciting your proxy to vote at the 2026 annual meeting of stockholders via live webcast (the “Annual Meeting”), including at any adjournments or postponements of the meeting. All stockholders will have the ability to access the proxy materials on the website referred to in the Notice, or request to receive a printed set of the proxy materials.

We intend to mail the Notice on or about March 26, 2026 to all stockholders of record entitled to vote at the Annual Meeting. The Notice contains instructions on how to access our Proxy Statement and our 2025 Annual Report on Form 10-K on the internet, instructions on how to vote via the internet or by telephone, instructions on how to request a paper copy of our proxy materials by mail, and how to register to attend the Annual Meeting.

Will I receive any other proxy materials by mail?

No, you will not receive any other proxy materials by mail unless you request, or had previously requested, a paper copy of proxy materials. To request that a full set of the proxy materials be sent to your specified postal address for the Annual Meeting, you may (i) visit www.proxyvote.com, (ii) call 1-800-579-1639 or (iii) send an email to sendmaterial@proxyvote.com. Please have your proxy card or Notice in hand when you access the website or call and follow the instructions provided and, if sending an email, please include your control number (discussed below) in the subject line.

What am I voting on?

There are four matters scheduled for a vote:

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Election of two Class II directors (“Proposal 1”);

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Ratification of the selection of Deloitte as our independent registered public accounting firm for the fiscal year ending December 31, 2026 (“Proposal 2”);

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Approval of an amendment and restatement of the 2024 Plan (“Proposal 3”); and

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Approval of an amendment and restatement of the 2024 ESPP (“Proposal 4”).

What if another matter is properly brought before the meeting?

The Board knows of no other matters that will be presented for consideration at the Annual Meeting. If any other matters are properly brought before the meeting, it is the intention of the persons named in the accompanying proxy to vote on those matters in accordance with their best judgment.

How does the Board of Directors recommend I vote on these matters?

Our Board of Directors recommends a vote:

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“FOR” the election of Raymond Sanchez, M.D. and Gwill York as Class II directors;

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“FOR” the ratification of the appointment of Deloitte as our independent registered public accounting firm for the fiscal year ending December 31, 2026;

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“FOR” the approval of an amendment and restatement of the 2024 Plan to treat outstanding pre-funded warrants the same as outstanding shares of Common Stock for purposes of calculating the number of shares to be automatically added to the share reserve thereunder pursuant to the “evergreen” feature of the 2024 Plan; and

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“FOR” the approval of an amendment and restatement of the 2024 ESPP to treat outstanding pre-funded warrants the same as outstanding shares of Common Stock for purposes of calculating the number of shares to be automatically added to the share reserve thereunder pursuant to the “evergreen” feature of the 2024 ESPP.

How do I attend the Annual Meeting?

The Annual Meeting will be held through a live webcast at www.virtualshareholdermeeting.com/ANRO2026. There is no physical meeting location, and thus you will not be able to attend the Annual Meeting in person.

You are entitled to attend the Annual Meeting if you were a stockholder of record as of the close of business on March 16, 2026, the record date, or hold a valid proxy for the meeting. To be admitted to the Annual Meeting, you will need to visit www.virtualshareholdermeeting.com/ANRO2026 and enter the 16‑digit Control Number found next to the label “Control Number” on your Notice, proxy card or voting instruction form. If you are a beneficial owner of shares registered in the name of your broker, bank, or other agent, follow the instructions from your broker, bank or other institution where you hold your account well in advance of the meeting if you have questions about obtaining your Control Number or proxy to vote.

Whether or not you participate in the Annual Meeting, it is important that you vote your shares. Please refer to the Q&A “How do I vote?” below for further details.

If you attend the Annual Meeting via live webcast with a Control Number, you will be able to vote at the meeting and submit questions. We encourage you to access the Annual Meeting before it begins at 8:30 a.m. Eastern Time. Online check-in will start approximately 15 minutes before the meeting on Tuesday, May 12, 2026.

Who can vote at the Annual Meeting?

Only stockholders of record at the close of business on March 16, 2026 will be entitled to vote at the Annual Meeting. On the record date, there were 31,945,516 shares of common stock outstanding and entitled to vote.

Stockholder of Record: Shares Registered in Your Name

If on March 16, 2026 your shares were registered directly in your name with Alto’s transfer agent, Equiniti Trust Company, LLC, then you are a stockholder of record. As a stockholder of record, you may vote online at the Annual Meeting or vote by proxy. Whether or not you plan to attend the Annual Meeting, to ensure your vote is counted, we urge you to vote by proxy over the telephone, vote by proxy through the internet or vote by proxy using a proxy card that you may request or that we may elect to deliver at a later time.

Beneficial Owner: Shares Registered in the Name of a Broker or Bank

If on March 16, 2026 your shares were held, not in your name, but rather in an account at a brokerage firm, bank or other similar organization, then you are the beneficial owner of shares held in “street name” and the Notice is being forwarded to you by that organization. The organization holding your account is considered to be the stockholder of record for purposes of voting at the Annual Meeting. As a beneficial owner, you have the right to direct your broker, bank or other agent regarding how to vote the shares in your account. You are also invited to attend the Annual Meeting, and may access the meeting and vote by logging in with your Control Number at www.virtualshareholdermeeting.com/ANRO2026. However, since you are not the stockholder of record, you must follow the instructions provided by your brokerage firm, bank or other similar organization for your bank, broker or other stockholder of record to vote your shares per your instructions. Alternatively, many brokers and banks provide the means to grant proxies or otherwise instruct them to vote your shares by telephone and via the internet, including by providing you with a Control Number via email or on your notice or your voting instruction form. If your shares are held in an account with a broker, bank or other stockholder of record providing such a service, you may instruct them to vote your shares by telephone (by calling the number provided in the Proxy Materials) or over the internet as instructed by your broker, bank or other stockholder of record. If you did not receive a control number via email or on your notice or voting instruction form and you wish to vote prior to or at the virtual Annual

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Meeting, you must follow the instructions from your broker, bank or other stockholder of record, including any requirement to obtain a valid legal proxy. Many brokers, banks and other stockholders of record allow a beneficial owner to obtain a valid legal proxy either online or by mail, and we recommend you contact your broker, bank or other stockholder of record to do so. You may not vote your shares online during the meeting unless you request and obtain a valid proxy from your broker or other agent, as required.

How do I vote?

For Proposal 1, you may either vote “For” the nominees to the Board or you may “Withhold” your vote for any nominee you specify. For Proposal 2, Proposal 3, and Proposal 4, you may vote “For” or “Against” or abstain from voting.

The procedures for voting are fairly simple:

Stockholder of Record: Shares Registered in Your Name

If you are a stockholder of record, you may vote at the Annual Meeting, or vote in advance by proxy over the telephone, vote by proxy through the internet, or vote by proxy using a proxy card that you may request. Whether or not you plan to attend the Annual Meeting, we urge you to vote by proxy to ensure your vote is counted. You may still attend the meeting and vote during the Annual Meeting even if you have already voted by proxy.

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To vote prior to the Annual Meeting (until 11:59 p.m. Eastern Time on May 11, 2026), you may vote via the Internet at www.proxyvote.com; by telephone; or by completing and returning their proxy card or voting instruction form, as described below.

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To vote through the internet prior to the Annual Meeting, go to www.proxyvote.com and follow the instructions to submit your vote on an electronic proxy card. You will be asked to provide the company number and Control Number from the Notice or proxy card. Your internet vote must be received by 11:59 p.m. Eastern Time on May 11, 2026 to be counted.

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To vote over the telephone, dial the number provided on the Notice or proxy card using a touch-tone phone and follow the recorded instructions. You will be asked to provide the company number and Control Number from your Notice or proxy card. Your telephone vote must be received by 11:59 p.m. Eastern Time on May 11, 2026 to be counted.

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To vote using the proxy card that may be requested, simply complete, sign and date the proxy card and return it promptly in the envelope provided. If you return your signed proxy card to us before the Annual Meeting, we will vote your shares as you direct.

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To vote during the Annual Meeting, if you are a stockholder of record as of the record date, follow the instructions at www.virtualshareholdermeeting.com/ANRO2026. You will need to enter the 16-digit Control Number found on your Notice or proxy card.

Beneficial Owner: Shares Registered in the Name of Broker or Bank

If you are a beneficial owner of shares registered in the name of your broker, bank or other agent, you should have received a voting instruction form from that organization rather than from Alto. You should follow the instructions in the notice to ensure your vote is counted. Alternatively, many brokers and banks provide the means to grant proxies or otherwise instruct them to vote your shares by telephone and via the internet, including by providing you with a Control Number via email or on notice or your voting instruction form. If your shares are held in an account with a broker, bank or other stockholder of record providing such a service, you may instruct them to vote your shares by telephone (by calling the number provided in the proxy materials) or over the internet as instructed by your broker, bank or other stockholder of record. If you did not receive a Control Number via email or on your notice or voting instruction form, and you wish to vote prior to or at the virtual Annual Meeting, you must follow the instructions from your broker, bank or other stockholder of record, including any requirement to obtain your Control Number. Many brokers, banks and other stockholders of record allow a beneficial owner to obtain their control number either online or by mail, and we recommend that you contact your broker, bank or other stockholder of record to do so.

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Internet proxy voting will be provided to allow you to vote your shares online, with procedures designed to ensure the authenticity and correctness of your proxy vote instructions. However, please be aware that you must bear any costs associated with your internet access, such as usage charges from internet access providers and telephone companies.

How many votes do I have?

On each matter to be voted upon, you have one vote for each share of common stock you own as of March 16, 2026.

If I am a stockholder of record and I do not vote, or if I return a proxy card or otherwise vote without giving specific voting instructions, what happens?

If you are a stockholder of record and do not vote by completing your proxy card, by telephone, through the internet or at the Annual Meeting, your shares will not be voted.

If you return a signed and dated proxy card or otherwise vote without marking voting selections, your shares will be voted, as applicable, “For” the election of both nominees for director, “For” the ratification of the selection by the Audit Committee of Deloitte as our independent registered public accounting firm for the fiscal year ending December 31, 2026, “For” the approval of an amendment and restatement of the 2024 Plan, and “For” the approval of an amendment and restatement of the 2024 ESPP. If any other matter is properly presented at the meeting, your proxyholder will vote your shares using his or her best judgment.

If I am a beneficial owner of shares held in street name and I do not provide my broker or bank with voting instructions, what happens?

If you are a beneficial owner of shares held in street name and you do not instruct your broker, bank or other agent how to vote your shares, your broker, bank or other agent may still be able to vote your shares in its discretion. Under the rules of the New York Stock Exchange (the “NYSE”), brokers, banks and other securities intermediaries that are subject to NYSE rules may use their discretion to vote your “uninstructed” shares with respect to matters considered to be “routine” under NYSE rules, but not with respect to “non-routine” matters. All brokers registered as members with the NYSE are subject to NYSE rules and, accordingly, the NYSE rules apply to the voting of all shares held in a brokerage account. In this regard, Proposal 1, Proposal 3, and Proposal 4 are considered to be “non-routine” under such rules, meaning that your broker may not vote your shares on this proposal in the absence of your voting instructions. However, Proposal 2 is considered to be a “routine” matter under such rules, meaning that if you do not return voting instructions to your broker by its deadline, your shares may be voted by your broker in its discretion on Proposal 2.

If you are a beneficial owner of shares held in street name, and you do not plan to attend the Annual Meeting, in order to ensure your shares are voted in the way you would prefer, you must provide voting instructions to your broker, bank or other agent by the deadline provided in the materials you receive from your broker, bank or other agent.

Will a list of the stockholders of record as of the record date be available?

For the ten days ending the day prior to the Annual Meeting, a list of our stockholders of record as of the close of business on the record date will be available for examination by any stockholders of record for a legally valid purpose at our corporate headquarters during regular business hours. To access the list of stockholders of record, please email generalcounsel@altoneuroscience.com.

Where can we get technical assistance?

If you encounter any difficulties accessing the Annual Meeting during the check-in or meeting time, please call the technical support number that will be posted on the virtual meeting login page.

During the Annual Meeting, how do we ask questions of management and the Board?

At the Annual Meeting, we plan to respond to appropriate stockholder questions relevant to Annual Meeting business, if allotted time permits. Stockholders of record as of the close of business on March 16,

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2026 may submit questions during the Annual Meeting after logging in with your Control Number through www.virtualshareholdermeeting.com/ANRO2026. To help ensure that we have a productive and efficient meeting, and in fairness to all stockholders in attendance, you will also find posted our rules of conduct for the Annual Meeting when you log in prior to the start of the Annual Meeting. If we receive substantially similar questions, we will group such questions together and provide a single response to avoid repetition. Questions that are not relevant to the proposals to be voted on at the Annual Meeting and in compliance with the rules of conduct for the Annual Meeting will not be responded to.

Who is paying for this proxy solicitation?

We will pay for the entire cost of soliciting proxies. In addition to these proxy materials, our directors and employees may also solicit proxies in person, by telephone, or by other means of communication. Directors and employees will not be paid any additional compensation for soliciting proxies. We may also reimburse brokerage firms, banks and other agents for the cost of forwarding proxy materials to beneficial owners.

What does it mean if I receive more than one Notice?

If you receive more than one Notice, your shares may be registered in more than one name or in different accounts. Please follow the voting instructions on all Notices to ensure that all of your shares are voted.

Can I change my vote after submitting my proxy?

Stockholder of Record: Shares Registered in Your Name

Yes. You can revoke your proxy at any time before the final vote at the meeting. If you are the record holder of your shares, you may revoke your proxy in any one of the following ways:

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You may submit another properly completed proxy card, dated with a later date.

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You may grant a subsequent proxy by telephone or through the internet.

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You may send a timely written notice that you are revoking your proxy to Alto’s Corporate Secretary at 650 Castro Street, Suite 450, Mountain View, California 94041.

•

You may vote online during the Annual Meeting. Simply attending the Annual Meeting without voting will not, by itself, revoke your proxy.

Your most current proxy card or telephone or internet proxy is the one that is counted.

Beneficial Owner: Shares Registered in the Name of Broker or Bank

If your shares are held by your broker, bank or other agent, you should follow the instructions provided to you by your broker, bank or other agent.

When are stockholder proposals due for next year’s Annual Meeting?

Our stockholders may submit proposals on matters appropriate for stockholder action at annual stockholder meetings in accordance with Rule 14a-8 promulgated under the Securities Exchange Act of 1934, as amended (the “Exchange Act”). For such proposals to be included in our proxy materials relating to our 2027 annual meeting of stockholders (the “2027 Annual Meeting”), all applicable requirements of Rule 14a-8 must be satisfied and your proposal must be submitted in writing by November 26, 2026 to our Corporate Secretary at 650 Castro Street, Suite 450, Mountain View, California 94041.

If you wish to submit a proposal or nominate a director at the 2027 Annual Meeting but you are not requesting that your proposal or nomination be included in our proxy materials for the 2027 Annual Meeting pursuant to Rule 14a-8 of the Exchange Act, your proposal or nomination must delivered to and received by our Corporate Secretary, in writing, at 650 Castro Street, Suite 450, Mountain View, California 94041 not later than the close of business on February 11, 2027 nor earlier than January 12, 2027. We also advise you to review our bylaws, which contain additional requirements about advance notice of stockholder proposals and director nominations.

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For more information, and for more detailed requirements, please refer to our Bylaws, filed as Exhibit 3.2 to our Current Report on Form 8-K (File No. 001-41944), filed with the SEC on February 6, 2024.

How are votes counted?

Votes will be counted by the inspector of election appointed for the Annual Meeting. For Proposal 1, the inspector of election will separately count votes “For,” “Withhold,” and broker non-votes. For Proposal 2, Proposal 3, and Proposal 4, the inspector of election will separately count votes “For” and “Against,” abstentions and, if applicable, broker non-votes.

Broker non-votes on all proposals will have no effect and will not be counted towards the vote total for these proposals. Abstentions on Proposal 2, Proposal 3, and Proposal 4 will have no effect and will not be counted towards the vote total for these proposals.

What are “broker non-votes”?

A “broker non-vote” occurs when your broker submits a proxy for the meeting with respect to “routine” matters but does not vote on “non-routine” matters because you did not provide voting instructions on these matters. These un-voted shares with respect to “non-routine” matters are counted as “broker non-votes” and are not counted towards the vote total for non-routine proposals. Proposal 1, Proposal 3, and Proposal 4 are considered to be “non-routine” under NYSE rules and we therefore expect some broker non-votes on these proposals. However, because Proposal 2 is considered “routine” under such rules, we do not expect broker non-votes on this proposal.

As a reminder, if you are a beneficial owner of shares held in street name, in order to ensure your shares are voted in the way you would prefer, you must provide voting instructions to your broker, bank or other agent by the deadline provided in the materials you receive from your broker, bank or other agent.

How many votes are needed to approve each proposal?

For Proposal 1, the election of directors, the nominees receiving the most “For” votes from the holders of shares present or represented by proxy and entitled to vote on the election of directors will be elected. Only votes “For” will affect the outcome of the vote. “Withhold” votes and broker non-votes will each have no effect on the outcome.

Approval of Proposal 2, the ratification of the selection by the Audit Committee of Deloitte as our independent registered public accounting firm for the fiscal year ending December 31, 2026, requires the affirmative vote of a majority of the votes cast on this proposal. Abstentions and broker non-votes are not considered votes cast and will have no effect on the outcome of Proposal 2. Since brokers have authority to vote on your behalf with respect to Proposal 2 as a “routine” matter, we do not expect broker non-votes on Proposal 2.

Approval of Proposal 3, the approval of an amendment and restatement of the 2024 Plan, requires the affirmative vote of a majority of the votes cast on this proposal. Abstentions and broker non-votes are not considered votes cast and will have no effect on the outcome of Proposal 3.

Approval of Proposal 4, the approval of an amendment and restatement of the 2024 ESPP, requires the affirmative vote of a majority of the votes cast on this proposal. Abstentions and broker non-votes are not considered votes cast and will have no effect on the outcome of Proposal 4.

What is the quorum requirement?

A quorum of stockholders is necessary to hold a valid meeting. A quorum will be present if stockholders holding at least a majority of the voting power of the outstanding shares entitled to vote are present at the Annual Meeting virtually or represented by proxy. On March 16, 2026, the record date, there were 31,945,516 shares of common stock outstanding and entitled to vote. A majority of these shares must be present in person or virtually or represented by proxy at the Annual Meeting to have a quorum.

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Abstentions and broker non-votes will be counted towards the quorum requirement. If there is no quorum, either the chairperson of the meeting or the holders of a majority of the voting power of the shares present at the meeting or represented by proxy may adjourn the Annual Meeting to another date.

How can I find out the results of the voting at the Annual Meeting?

Preliminary voting results will be announced at the Annual Meeting. In addition, final voting results will be published in a current report on Form 8-K that we expect to file with the SEC within four business days after the Annual Meeting. If final voting results are not available to us within four business days after the meeting, we intend to first file a Form 8-K publishing preliminary results and, within four business days after the final results are known to us, file an additional Form 8-K to publish the final results.

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PROPOSAL 1

ELECTION OF DIRECTORS

Our Board is divided into three classes, with one class of our directors standing for election each year. The members of each class are elected to serve a three-year term with the term of office of each class ending in successive years. The Board presently has six members. The Board has nominated, based on the recommendation of the Nominating and Corporate Governance Committee (the “Governance Committee”), two Class II directors to stand for election at the Annual Meeting: Dr. Raymond Sanchez and Gwill York. Both nominees are currently directors of the Company. Dr. Raymond Sanchez was appointed by the Board in August 2025 after being identified and evaluated by members of the Board and management team, and Ms. York was previously elected by our stockholders. If elected at the Annual Meeting, each nominees would serve until the 2029 annual meeting and until the director’s successor has been duly elected and qualified or, if sooner, until the director’s death, resignation or removal.

Directors are elected by a plurality of the votes of the holders of shares present at the Annual Meeting or represented by proxy and entitled to vote on the election of directors. Accordingly, the two nominees receiving the highest number of affirmative votes will be elected. Shares represented by executed proxies will be voted, if authority to do so is not withheld, for the election of the two nominees named below. We have no reason to believe that our director nominees will be unavailable for election at the Annual Meeting. In the event that either of our director nominees is unexpectedly not available to serve, proxies may be voted for another person nominated as a substitute by the Board, or the Board may reduce the number of directors to be elected at the Annual Meeting.

On March 16, 2026, our Board approved an expansion of the size of the Board of Directors from six to seven directors, in accordance with a Securities Purchase Agreement that we entered into with certain institutional investors, dated March 16, 2026, pursuant to which we issued and sold shares of our common stock and pre-funded warrants to purchase shares of our common stock with an aggregate purchase price of approximately $120 million. All vacancies on the board of directors are filled exclusively by the affirmative vote of a majority of the remaining directors, even if less than a quorum is present, and not by the stockholders. Your proxy cannot be voted for a greater number of persons than the number of director nominees named in this proxy statement. A director elected by the Board to fill a vacancy in a class, including vacancies created by an increase in the number of directors, shall serve for the remainder of the full term of that class and until the director’s successor is duly elected and qualified or such director’s earlier death, resignation or removal.

Our corporate governance guidelines encourage our Board, including the nominees for director, to attend our annual meetings. Information relating to the director nominees and each continuing director, including his or her period of service as a director of the Company, principal occupation and other biographical material is shown below.

Class II Nominees to the Board of Directors for a Three-Year Term Expiring at the 2029 Annual Meeting

The nominees, their respective ages as of March 26, 2026, and the class in which they are being nominated are provided in the table below. Additional biographical description of the nominees, including length of service, is set forth in the text below the table. The description includes primary individual experience, qualifications, qualities and skills of our nominees that led to the conclusion that each should serve as a member of our Board at this time.

Name of Director Nominee

Class

Age

Position

Raymond Sanchez, M.D.

Director

Gwill York

Director

Raymond Sanchez, M.D has served as a member of our board of directors since August 2025. Dr. Sanchez has served as a Senior Advisor at Bain Capital Life Sciences, a global investment firm, since September 2024. He has also served as a director of Rapport Therapeutics, Inc. (Nasdaq: RAPP), a clinical-stage biotechnology company, since November 2024, and serves on the board of numerous privately held biotechnology companies. Dr. Sanchez previously served as Chief Medical Officer of Cerevel Therapeutics

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Holdings, Inc. (previously Nasdaq: CERE), from January 2019 to August 2024 when it was acquired by AbbVie Inc., and of Avanir Pharmaceuticals, Inc. from June 2018 to January 2019. From November 2007 to January 2019, Dr. Sanchez held various roles of increasing responsibility at Otsuka Pharmaceutical Development & Commercialization, Inc., a privately-held healthcare company. Dr. Sanchez was an executive co-chair of the International Society for CNS Drug Development from November 2017 to January 2022 and has also contributed to other academic and charitable organizations. Dr. Sanchez holds two degrees from Northwestern University, a Bachelor of Arts degree in psychology from the Weinberg College of Arts and Sciences and a medical degree from the Feinberg School of Medicine, and trained in psychiatry at the Yale School of Medicine. The Board believes that Dr. Sanchez’s extensive experience overseeing medical strategy in the biotechnology and pharmaceutical industries and his background in medicine qualify him to serve on our Board.

Gwill York has served as a member of our board of directors since September 2021. From 1994 to 2017, Ms. York served as Founding Managing Director of Lighthouse Capital Partners, a venture financing firm she co-founded. Ms. York currently serves as a member of the board of directors of Sofina SA, a Belgian investment company listed on Euronext Brussels, as well as a member of the boards of trustees of various medical and non-profit organizations. Ms. York received an M.B.A. from Harvard Business School and a B.A. in Urban and Developing Economics from Harvard University. Our board of directors believes that Ms. York’s investment experience at Lighthouse Capital, financial expertise, and history of advising early-stage healthcare and technology companies qualify her to serve on our board of directors.

The Board Of Directors Recommends
A Vote In Favor Of The Named Nominees.

Continuing Directors

Continuing directors, their respective ages as of March 26, 2026, and the class in which they belong are provided in the table below. Additional biographical descriptions of each director, including length of service, are set forth in the text below the table.

Name of Director

Class

Age

Position

Term
Expires

Amit Etkin, M.D., Ph.D.

III

President, Chief Executive Officer, and Chair of the Board

2027

Christopher Nixon Cox

III

Lead Independent Director

2027

Andrew Dreyfus

Director

2028

Husseini Manji, M.D.

Director

2028

Amit Etkin, M.D., Ph.D. is our Founder and has served as our Chief Executive Officer and the Chair of our board of directors since March 2019 and as our President since November 2023. Prior to forming Alto, Dr. Etkin served as a Professor of Psychiatry and Behavioral Sciences at the Stanford University School of Medicine, where he was on staff in multiple leading roles since July 2010. As a tenured Professor, Dr. Etkin became an international leader in the neuroscience of psychiatric disorders and their treatments. Dr. Etkin completed his psychiatry training at Stanford University and received an M.D. and a Ph.D. in Neurobiology from Columbia University, an M.Phil. in Neurobiology from Columbia University, and a B.S. in Biology from the Massachusetts Institute of Technology. Our board of directors believes that Dr. Etkin’s experience as our Founder, President, and Chief Executive Officer, as well as his expertise in the field of neuroscience, qualify him to serve on our board of directors.

Christopher Nixon Cox has served as a member of our board of directors since April 2022. Since December 2021, Mr. Cox has served as Chief Executive Officer of Lightswitch Capital, a private equity firm. In addition, Mr. Cox has served as Chief Executive Officer of Argali Carbon Corporation, a carbon offset developer, since January 2023 and of BioSource Feeds Corporation since November 2023. From December 2018 until March 2020, Mr. Cox served as Vice Chairman of Brightsphere, Inc, a publicly traded asset manager. Mr. Cox has also served as the Managing Partner and co-founder of OC Global Partners LLC, a financial services company, since October 2006. Previously, Mr. Cox served as a corporate associate

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at the law firm of Weil, Gotshal & Manges LLP from 2004 to 2006. Mr. Cox has served as chairman and a member of the board of directors of High-Trend International Group (Nasdaq: HTCO), an international shipping company, since March 2025 and as a member of the board of directors of Newsmax Inc. (NYSE: NMAX), a multimedia company, since December 2020. Mr. Cox received a J.D. from the New York University School of Law, a certificate in Finance from New York University Stern School and a B.A. in Politics from Princeton University. Our board of directors believes that Mr. Cox’s financial expertise and investment experience qualify him to serve on our board of directors.

Andrew Dreyfus has served as a member of our board of directors since October 2023. Since October 2025, Mr. Dreyfus has served as President and Chief Executive Officer of the National Institute for Health Care Management (NIHCM) Foundation. From August 2005 to December 2022, Mr. Dreyfus served in roles of increasing responsibility at Blue Cross Blue Shield of Massachusetts, a health insurance company, most recently serving as President and Chief Executive Officer from September 2010 to December 2022. Mr. Dreyfus served as a member of the board of directors of Ironwood Pharmaceutics, Inc. (Nasdaq: IRWD), a pharmaceutical company, from April 2016 to November 2025. He currently serves on numerous boards and advisory boards for non-profit organizations. Mr. Dreyfus received a B.A. in English from Connecticut College. Our board of directors believes that Mr. Dreyfus’ extensive leadership experience in the healthcare industry and his service as a public company director qualify him to serve on our board of directors.

Husseini Manji, M.D. has served as a member of our board of directors since February 2024. Since May 2023, Dr. Manji has served as Co-Chair of the U.K. Government Mental Health Mission. Dr. Manji has served as a professor at the University of Oxford since June 2021 and has served as a visiting professor at Duke University School of Medicine since July 2006. Dr. Manji previously served as Global Head, Science for Minds at Johnson & Johnson, a pharmaceutical company, from July 2020 to July 2022. Dr. Manji served as Global Therapeutic Head, Neuroscience at the Janssen Pharmaceutical Companies of Johnson & Johnson, a pharmaceutical company, from June 2008 to July 2020. Dr. Manji received an M.D. from the University of British Columbia and a B.S. in Biochemistry from the University of British Columbia. Dr. Manji received the designation of Fellow of the Royal College of Physicians of Canada from the Royal College of Physicians and Surgeons of Canada. Our board of directors believes Dr. Manji’s expertise and experience in the field of neuroscience qualify him to serve on our board of directors.

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BOARD OF DIRECTORS AND CORPORATE GOVERNANCE

Independence of the Board of Directors

Our Board has undertaken a review of the independence of our directors and considered whether any director has a relationship that, in the opinion of the board of directors, would interfere with the exercise of independent judgment in carrying out the responsibilities of a member of our board. Based upon information requested from and provided by each director concerning such director’s background, employment, and affiliations, including family relationships, our board of directors has determined that Mr. Cox, Mr. Dreyfus, Dr. Manji, Dr. Sanchez, and Ms. York, representing five of our six current directors, are “independent directors” as defined under the listing standards of the NYSE. In making these determinations, our Board considered the current and prior relationships that each director has with our company and all other facts and circumstances that our board of directors deemed relevant in determining their independence, including the beneficial ownership of our capital stock by each non-employee director and the transactions described in the section titled “Certain Related Person Transactions and Indemnification” below. Our Board has determined that Dr. Etkin, by virtue of his role as our President and Chief Executive Officer, is not an independent director under the current rules and regulations of the SEC and the listing standards of the NYSE. There are no family relationships among any of our directors or executive officers.

Board Leadership Structure

Dr. Etkin, our Founder, President, and Chief Executive Officer, is Chair of the Board. Our Board believes that combining the positions of Chief Executive Officer and Chair of the Board helps to ensure that the Board and management act with a common purpose. Our Board also believes that it is advantageous to have a chair of the board of directors with an extensive history with, and knowledge of, our company (as is the case with Dr. Etkin).

As Dr. Etkin is not an independent director, our Board has appointed Mr. Cox to serve as our lead independent director. The lead independent director’s responsibilities include, but are not limited to: presiding over all meetings of the Board at which the Chair of the Board is not present, including any executive sessions of the independent directors; calling meetings or separate sessions of the independent directors; approving board meeting schedules and agendas; acting as the liaison between the independent directors and the Chief Executive Officer and Chair of the Board; and when appropriate, meeting or otherwise communicating with our major stockholders or other constituencies. Our corporate governance guidelines provide the flexibility for our Board to modify our leadership structure in the future as it deems appropriate.

In addition, we have a separate chair for each committee of our Board. The chair of each committee is expected to report regularly to our Board on the activities of their committee in fulfilling their responsibilities as detailed in their respective charters or specify any shortcomings should that be the case.

Director Commitments

Our Board believes that all members of the Board should have sufficient time and attention to devote to Board duties and to otherwise fulfill the responsibilities required of directors. In assessing whether directors and nominees for director have sufficient time and attention to devote to Board duties, the Governance Committee and our Board consider, among other things, whether directors may be “overboarded,” which refers to the situation where a director serves on an excessive number of boards.

Our Board believes that each of our directors, including our director nominee, has demonstrated the ability to devote sufficient time and attention to Board duties and to otherwise fulfill the responsibilities required of directors.

Role of the Board of Directors in Risk Oversight

One of the Board’s key functions is informed oversight of our risk management process. The Board does not have a standing risk management committee, but rather administers this oversight function directly through the Board as a whole, as well as through the standing committees of the Board that address risks

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inherent in their respective areas of oversight. In particular, our Board is responsible for monitoring and assessing strategic risk exposure, including a determination of the nature and level of risk appropriate for us.

Our Audit Committee has the responsibility to consider and discuss our guidelines and policies with respect to risk assessment and risk management, including our major financial risk exposures and the steps our management has taken to monitor and control these exposures, including guidelines and policies to govern the process by which risk assessment is undertaken and the execution of internal controls. The Audit Committee also monitors compliance with legal and regulatory requirements, in addition to oversight of our compliance with the Sarbanes-Oxley Act of 2002, as amended. Audit Committee responsibilities also include oversight of cybersecurity risk management, and, to that end, the Audit Committee discusses cybersecurity and IT risk management periodically with management as part of standing meeting agendas. Our Governance Committee monitors the effectiveness of our corporate governance guidelines. Our Compensation and Management Development Committee assesses and monitors whether any of our compensation policies and programs has the potential to encourage excessive risk-taking. Typically, the entire Board or the applicable committee of the Board, meets periodically, and at least annually, with the employees responsible for risk management in the committees’ respective areas of oversight. Both the Board as a whole and the various standing committees receive periodic reports from management as to various risk management topics, as well as incident reports as matters may arise. It is the responsibility of the committee chairs to report findings regarding material risk exposures to the Board.

Meetings of the Board of Directors

The Board met eight times during the last fiscal year. Each Board member attended 75% or more of the aggregate number of meetings of the Board and of the committees on which he or she served, held during the portion of the last fiscal year for which he or she was a director or committee member.

As required under applicable NYSE listing standards, in fiscal year 2025, our independent directors met at regularly scheduled executive sessions without management present. Mr. Cox presided over the executive sessions.

Information Regarding Committees of the Board of Directors

The Board has established three standing committees: an Audit Committee, a Compensation and Management Development Committee, and a Nominating and Corporate Governance Committee. Members serve on these committees until their resignation or until otherwise determined by our Board. Our Board may establish other committees as it deems necessary or appropriate from time to time.

Each committee operates under a written charter that is available to our stockholders in the “Corporate Governance” section of our investor relations website at https://investors.altoneuroscience.com, which satisfies the applicable rules and regulations of the SEC and the listing standards of the NYSE. The following table provides membership and meeting information for each of these standing committees:

Name

Audit

Compensation and
Management Development

Nominating and
Corporate
Governance

Christopher Nixon Cox

Andrew Dreyfus

Husseini Manji, M.D.

Raymond Sanchez, M.D.

Gwill York

Total meetings in fiscal year 2025

Designates Committee Chairperson

Each of the committees has authority to engage legal counsel or other experts or consultants as it deems appropriate to carry out its responsibilities.

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Audit Committee

Our Audit Committee consists of Mr. Cox, Mr. Dreyfus, and Ms. York, with Ms. York serving as the chair. Our Board has determined that each of these individuals satisfies the requirements for independence under the current rules and regulations of the SEC and the listing standards of the NYSE. Each member of our Audit Committee can read and understand fundamental financial statements in accordance with NYSE audit committee requirements. In addition, our Board has determined that Mr. Cox and Ms. York each qualify as an “audit committee financial expert” within the meaning of SEC regulations. In arriving at these determinations, the Board has examined each Audit Committee member’s scope of experience and the nature of their prior and/or current employment.

The primary responsibilities of the audit committee include, among other things:

•

helping our board of directors oversee our corporate accounting and financial reporting processes;

•

managing the selection, engagement, qualifications, independence, and performance of a qualified firm to serve as the independent registered public accounting firm to audit our financial statements;

•

discussing the scope and results of the audit with the independent registered public accounting firm, and reviewing, with management and the independent accountants, our interim and year-end operating results;

•

developing procedures for employees to submit concerns anonymously about questionable accounting or audit matters;

•

reviewing related person transactions;

•

obtaining and reviewing a report by the independent registered public accounting firm that describes its internal quality control procedures, any material issues with such procedures, and any steps taken to deal with such issues when required by applicable law; and

•

approving, or, as permitted, pre-approving, audit and permissible non-audit services to be performed by the independent registered public accounting firm.

Report of the Audit Committee of the Board of Directors(1)

The Audit Committee has reviewed and discussed the consolidated audited financial statements for the fiscal year ended December 31, 2025 with management of the Company. The Audit Committee has discussed with the Company’s independent registered public accounting firm the matters required to be discussed by the applicable requirements of the Public Company Accounting Oversight Board (“PCAOB”) and the SEC. The Audit Committee has also received the written disclosures and the letter from the independent registered public accounting firm required by applicable requirements of the PCAOB regarding the independent accountants’ communications with the Audit Committee concerning independence, and has discussed with the independent registered public accounting firm the accounting firm’s independence. Based on the foregoing, the Audit Committee has recommended to the Board of Directors that the consolidated audited financial statements be included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2025.

The Audit Committee

Ms. Gwill York, Chair
Mr. Christopher Nixon Cox
Mr. Andrew Dreyfus

(1)

The material in this report is not “soliciting material,” is not deemed “filed” with the SEC and is not to be incorporated by reference in any filing of the Company under the Securities Act of 1933, as amended (the “Securities Act”), or the Exchange Act, whether made before or after the date hereof and irrespective of any general incorporation language in any such filing.

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Compensation and Management Development Committee (“Compensation Committee”)

Our Compensation Committee consists of Mr. Cox, Mr. Dreyfus, and Ms. York, with Mr. Cox serving as chair. Our Board has determined that each of the members of our Compensation Committee is independent under the listing standards of the NYSE and qualifies as a “non-employee director” as defined in Rule 16b-3 promulgated under the Exchange Act.

The primary responsibilities of the Compensation Committee include, among other things:

•

reviewing and approving (or, as applicable, recommending to our board of directors) the compensation of our Chief Executive Officer and other executive officers;

•

reviewing and approving the compensation paid to our non-employee directors;

•

administering our equity incentive plans and other benefit programs;

•

reviewing and approving, or making recommendations to our board of directors with respect to, incentive compensation and equity plans;

•

reviewing, adopting, amending, and terminating the terms of any employment agreements, severance arrangements, bonus plans, deferred compensation plans, change-of-control protections, and any other compensatory arrangements for our executive officers;

•

reviewing, evaluating, and recommending to our board of directors succession plans for our executive officers; and

•

reviewing and establishing general policies relating to compensation and benefits of our employees, including our overall compensation philosophy.

Compensation Committee Processes and Procedures

Typically, the Compensation Committee holds regularly scheduled meetings several times per year. The agenda for each meeting is developed by the Chair of the Compensation Committee, in consultation with management and our outside compensation consultants. The Compensation Committee meets regularly in executive session. Various members of management and other employees as well as outside advisors or consultants may be invited by the Compensation Committee to present financial, equity, market comparative or other background information or advice, or to otherwise participate in Compensation Committee meetings.

The Chief Executive Officer may not participate in, or be present during, any deliberations or determinations of the Compensation Committee regarding his compensation. The charter of the Compensation Committee grants the Compensation Committee full access to all of our books, records, facilities and personnel. In addition, under the charter, the Compensation Committee has the authority to obtain, at our expense, advice and assistance from compensation consultants and internal and external legal, accounting or other advisors and other external resources that the Compensation Committee considers necessary or appropriate in the performance of its duties. The Compensation Committee has direct responsibility for the oversight of the work of any consultants or advisers engaged for the purpose of advising the Compensation Committee. In particular, the Compensation Committee has the sole authority to retain, in its sole discretion, compensation consultants to assist in its evaluation of executive and director compensation, including the authority to approve the consultant’s reasonable fees and other retention terms.

For the fiscal year ended December 31, 2025, the Compensation Committee retained an independent compensation consultant from Aon Consulting, Inc., through its Human Capital Solutions division (“Aon”), as the Compensation Committee’s advisor reporting directly to the Chair of the Compensation Committee. The Compensation Committee annually assesses the independence of the compensation consultant under SEC and NYSE criteria and, for 2025, concluded that no conflict of interest exists that would prevent Aon from serving as an independent consultant to the Compensation Committee.

Our Compensation Committee identified Aon based on Aon’s consulting experience, key competencies, technical resources, and general reputation in the industry. The Compensation Committee requested that Aon:

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•

evaluate the efficacy of our compensation strategy and practices in supporting and reinforcing our long-term strategic goals;

•

assist in both refining our compensation strategy and developing and implementing executive and director compensation programs to execute that strategy;

•

assist the Compensation Committee in formulating strategies for fostering retention and strengthening alignment of compensation with the achievement of specific strategic milestones and stockholder value creation; and

•

ensure our compensation strategy adheres to market best practices.

As part of its engagement of Aon, the Compensation Committee directed Aon to develop a comparative group of companies and to perform analyses of competitive performance and compensation levels for that group. Aon ultimately developed recommendations that were presented to the Compensation Committee for its consideration.

Historically, the Board or the Compensation Committee has made most of the significant adjustments to annual compensation, determined bonus and equity awards, and established new performance objectives at one or more meetings held during the first quarter of the year. However, the Compensation Committee also considers matters related to individual compensation, such as compensation for new executive hires, as well as high-level strategic issues, such as the efficacy of our compensation strategy, potential modifications to that strategy and new trends, plans or approaches to compensation, at various meetings throughout the year. For executives other than the Chief Executive Officer, the Compensation Committee solicits and considers evaluations and recommendations submitted to the Compensation Committee by the Chief Executive Officer. In the case of the Chief Executive Officer, the evaluation of his performance is conducted by the Compensation Committee, which determines any adjustments to his compensation as well as awards to be granted with input from directors.

Nominating and Corporate Governance Committee (“Governance Committee”)

Our Governance Committee currently consists of Dr. Manji, Mr. Cox and Dr. Sanchez, with Dr. Manji serving as Chair. Our Board has determined that each of these individuals is “independent” as defined under the applicable listing standards of the NYSE and SEC rules and regulations.

The primary responsibilities of the Governance Committee include, among other things:

•

identifying, reviewing, and evaluating candidates, including the nomination of incumbent directors for reelection and nominees recommended by our stockholders, to serve on our board of directors;

•

considering and making recommendations to our board of directors regarding the composition and chairmanship of the committees of our board of directors;

•

instituting plans or programs for the continuing education of our board of directors and orientation of new directors;

•

developing and making recommendations to our board of directors regarding corporate governance guidelines and matters; and

•

overseeing periodic evaluations of the board of directors’ performance, including committees of the board of directors.

Board Membership Criteria

The Board and the Governance Committee will determine the appropriate characteristics, skills and experience for the Board as a whole and for its individual members. The Board considers recommendations for nominees from the Governance Committee. In considering candidates, the Board and the Governance Committee intend to consider such factors as possessing relevant expertise upon which to be able to offer advice and guidance to management, having sufficient time to devote to our affairs, demonstrated excellence in his or her field, having the ability to exercise sound business judgment, having a diverse personal background, perspective and experience, and having the commitment to rigorously represent the long-term

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interests of our stockholders. The Board and the Governance Committee review candidates for director nomination in the context of the current composition of our Board, our operating requirements and the long-term interests of our stockholders. In conducting this assessment, the Board and the Governance Committee will consider diversity of personal background, perspective and experience, age, skills, and such other factors as each deems appropriate given the current needs of us and our Board to maintain a balance of knowledge, experience and capability. With regard to diversity, we are committed to seeking to attain diversity and balance among directors of thought, viewpoints, backgrounds, skills, experience, expertise, race, gender, sexual orientation, and geography. Accordingly, as part of the director search process, the Governance Committee will endeavor to consider qualified candidates, including candidates who self-identify their gender as female and candidates from underrepresented communities, in each case who meet the relevant business and search criteria. The Governance Committee assesses the effectiveness of such policy through its periodic evaluation of the composition of the full board of directors.

In the case of incumbent directors whose terms of office are set to expire, the Board and the Governance Committee review such directors’ overall service to us and our business during their term, including the number of meetings attended, level of participation, quality of performance, and any other relationships and transactions that might impair such directors’ independence, including share ownership or other factors. In the case of new director candidates, the Board and the Governance Committee also determine whether the nominee must be independent for purposes of satisfying NYSE rules and regulations.

The Governance Committee will consider director candidates recommended by stockholders. The Governance Committee does not intend to alter the manner in which it evaluates candidates, including the minimum criteria set forth above, based on whether or not the candidate was recommended by a stockholder. Stockholders who wish to recommend individuals for consideration by the Governance Committee to become nominees for election to the Board may do so by delivering a written recommendation to the Governance Committee at the following address: 650 Castro Street, Suite 450, Mountain View, California 94041 in accordance with the timeline outlined in the section entitled “When are stockholder proposals due for next year’s Annual Meeting?” under the heading “Questions and Answers About These Proxy Materials and Voting.” Submissions must include the full name of the proposed nominee, a description of the proposed nominee’s business experience for at least the previous five years, complete biographical information, a description of the proposed nominee’s qualifications as a director and a representation that the nominating stockholder is a beneficial or record holder of our stock and has been a holder for at least one year. Any such submission must be accompanied by the written consent of the proposed nominee to be named as a nominee and to serve as a director if elected.

Non-Employee Director Compensation

Director Compensation Table

The following table sets forth information regarding the compensation of our non-employee directors earned for service on our Board during the year ended December 31, 2025.

Name	Fees Earned or Paid in Cash ($)(1)		Option Awards ($)(2)		Total ($)
Po Yu (Jeff) Chen, Ph.D.*		19,747		—		19,747
Christopher Nixon Cox		4,390		106,153		110,543
Andrew Dreyfus		54,000		26,263		80,263
Husseini Manji, M.D.		1,929		71,200		73,129
Maha Radhakrishnan, M.D.*		17,906		—		17,906
Raymond Sanchez, M.D.		8,682		76,222		84,904
Gwill York		—		88,178		88,178

Dr. Chen and Dr. Radhakrishnan served as members of our Board until their terms of office expired at our May 13, 2025 Annual Meeting of Stockholders.

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(1)

Consists of cash compensation paid to non-employee directors during 2025 including annual cash retainers, committee chair retainers, and committee member retainers. Certain directors elected to receive stock options in lieu of all or a portion of such 2025 cash retainers, which had a grant date fair value, calculated based on the Black-Scholes option valuation methodology, equal to the compensation that they would have otherwise received in cash.

(2)

The amounts shown in the Option Awards column represent the grant date fair value of stock options granted to the non-employee director during 2025 under the 2024 Equity Incentive Plan. Amounts reported in this column have been determined in accordance with Financial Accounting Standards Board Accounting Standards Codification, Topic 718. The assumptions made in the valuation reflected in this column are set forth in Note 11 to our consolidated financial statements included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2025. The amounts do not reflect dollar amounts actually received by the non-employee director or the economic value that may be received by the non-employee director upon stock option exercise or any sale of the underlying shares of common stock. Options held by non-employee members of the Board were not eligible for the Repricing described below under “Executive Compensation—Narrative to the Summary Compensation Table—Option Repricing.”

The following table provides information regarding the number of shares of common stock underlying options held by our non-employee directors that were outstanding as of December 31, 2025:

Name	Shares Underlying Outstanding Options as of December 31, 2025
Po Yu (Jeff) Chen, Ph.D.*		—
Christopher Nixon Cox		75,720
Andrew Dreyfus		68,342
Husseini Manji, M.D.		63,139
Maha Radhakrishnan, M.D.*		—
Raymond Sanchez, M.D.		34,502
Gwill York		113,463

Dr. Chen and Dr. Radhakrishnan served as members of our Board until their terms of office expired at our May 13, 2025 Annual Meeting of Stockholders.

Dr. Etkin, our Chief Executive Officer, who is also the Chair of the Board of Directors, did not receive any additional compensation for service as a director. Dr. Etkin’s compensation as a named executive officer is set forth below under “Executive Compensation—Summary Compensation Table.”

Non-Employee Director Compensation Policy

For the year ended December 31, 2025, our non-employee director compensation policy provided that each non-employee director would receive the following compensation for service on our Board:

•

an annual cash retainer of $40,000 (plus an additional $30,000 for the non-executive chair of our Board, if any, and an additional $20,000 for the lead independent director);

•

an additional annual cash retainer of $8,000, $6,000, and $5,000 for service as a member of the Audit Committee, the Compensation Committee, and the Governance Committee, respectively;

•

an additional annual cash retainer of $16,000, $12,000, and $10,000 for service as chair of the Audit Committee, the Compensation Committee, and the Governance Committee, respectively;

•

an initial option grant to purchase 30,574 shares of our common stock on the date of each such non-employee director’s appointment to our Board; and

•

an annual option grant to purchase 15,287 shares of our common stock on the date of each of our annual stockholder meetings.

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Under the non-employee director compensation policy, directors may elect to receive some or all of their eligible cash compensation in the form of stock options.

Upon appointment of Dr. Sanchez to the board of directors on August 12, 2025, pursuant to the non-employee director compensation policy described above, Dr. Sanchez received an option to purchase 30,574 shares of our common stock under our 2024 Equity Incentive Plan at an exercise price per share equal to $3.18.

Each of the option grants described above under the non-employee director compensation policy was granted under our 2024 Equity Incentive Plan. Each initial option grant will vest and become exercisable in equal monthly installments over a three-year period, subject to the director’s continuous service to us through each vesting date. Each annual option grant will vest and become exercisable subject to the director’s continuous service to us through the earlier of the first anniversary of the date of grant or the next annual stockholder meeting. The term of each option will be ten years, subject to earlier termination as provided in the 2024 Equity Incentive Plan.

We have reimbursed and will continue to reimburse all of our non-employee directors for their reasonable out-of-pocket expenses incurred in attending Board and committee meetings.

Our non-employee director compensation policy was subsequently amended by our Board on November 11, 2025 to modify the equity grants made to non-employee directors under the Plan. Beginning January 1, 2026, our non-employee director compensation policy provides that each non-employee director will receive the following:

•

an initial option grant to purchase the lesser of: (i) 48,200 shares of our common stock or (ii) the largest whole number shares of our common stock that results in such option having an aggregate Black-Scholes value not exceeding $400,000 on the date of each such non-employee director’s appointment to our Board; and

•

an annual option grant to purchase the lesser of: (1) 24,100 shares of our common stock or (2) the largest whole number shares of our common stock that results in such option having an aggregate Black-Scholes value not exceeding $200,000 shares of our common stock on the date of each of our annual stockholder meetings.

Stockholder Communications with the Board of Directors

All stockholders and other interested parties are welcome to communicate with our non-management directors through an established process for stockholder communication. For communication directed to our non-management directors, please contact our Corporate Secretary in writing at the address listed below.

Alto Neuroscience, Inc.
650 Castro Street, Suite 450
Mountain View, CA 94041
Attn: Corporate Secretary

Communications from stockholders must set forth:

the name and address of the stockholder on whose behalf the communication is sent; and

the number and class of shares of the Company that are owned beneficially by such stockholder as of the date of the communication.

The Corporate Secretary will review each communication. The Corporate Secretary will forward such communication to the Board or to any individual director to whom the communication is addressed unless the communication contains advertisements or solicitations or is unduly hostile, threatening or similarly inappropriate, in which case the Corporate Secretary shall discard the communication. All communications directed to the Audit Committee in accordance with the Company’s whistleblower policy that relate to questionable accounting or auditing matters involving the Company will be promptly and directly forwarded to the Audit Committee.

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Code of Business Conduct and Ethics

We have adopted a written code of business conduct and ethics (the “Code of Conduct”) that applies to our directors, officers, and employees, including our principal executive officer, principal financial officer, principal accounting officer or controller, or person performing similar functions. A copy of the Code of Conduct is available in the “Corporate Governance” section of our investor relations website at https://investors.altoneuroscience.com. We intend to disclose on our website any future amendments of our Code of Conduct or waivers that exempt any of the principal executive officer, principal financial officer, principal accounting officer or controller, persons performing similar functions or our directors from provisions in the Code of Conduct. Information contained on, or that can be accessed through, our website is not incorporated by reference into this Proxy Statement.

Insider Trading Policy

We have adopted insider trading policies and procedures governing the purchase, sale, and/or other dispositions of our securities by directors, officers, and employees, or the Company itself, that are reasonably designed to promote compliance with insider trading laws, rules, and regulations, and the NYSE listing standards. A copy of our Insider Trading Policy was filed as Exhibit 19.1 to our Annual Report on Form 10-K for the fiscal year ended December 31, 2024 filed on March 20, 2025.

Corporate Governance Guidelines

We have adopted Corporate Governance Guidelines to ensure that the Board will have the necessary authority and practices in place to review and evaluate our business operations as needed and to make decisions that are independent of our management. The guidelines are also intended to align the interests of directors and management with those of our stockholders. The Corporate Governance Guidelines set forth the practices the Board intends to follow with respect to, among other things, board composition and selection including diversity, board meetings and involvement of senior management, Chief Executive Officer performance evaluation and succession planning, and board committees and compensation. The Corporate Governance Guidelines are available in the “Corporate Governance” section of our investor relations website at https://investors.altoneuroscience.com.

Hedging and Pledging Policy

Our Board has adopted an insider trading policy which applies to all of our directors, officers, employees, and agents (such as consultants and contractors). The policy prohibits hedging or similar transactions designed to decrease the risks associated with holding our common stock. In addition, our insider trading policy prohibits trading in derivative securities related to our common stock, which include publicly traded call and put options, engaging in short selling of our common stock, holding our common stock in a margin account, and pledging our shares as collateral for a loan.

Equity Award Grant Policies and Procedures

It is not the Compensation Committee’s practice to time or otherwise coordinate the granting of any equity awards to our non-employee directors or named executive officers with any release of material nonpublic information. It is the practice of our Compensation Committee to review the Company’s results and our named executive officers’ performance following the end of a fiscal year, as well as the outstanding equity awards held by our named executive officers, and, based on those reviews, to grant stock options to our named executive officers. The grant date for those equity awards is generally consistent with the date on which our Compensation Committee meets during the first fiscal quarter of each year. Additionally, our Compensation Committee approves the granting of equity awards in connection with the commencement of employment of our named executive officers, and from time to time as determined appropriate by our Compensation Committee. In accordance with our non-employee director compensation policy, our eligible non-employee directors are granted stock options on the effective date of their appointment to the board, the date of each annual meeting of our stockholders, and on specifically designated dates for any director who elects to receive some or all of their eligible cash compensation in the form of stock options.

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PROPOSAL 2

RATIFICATION OF SELECTION OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

The Audit Committee of the Board has selected Deloitte & Touche LLP (“Deloitte”) as our independent registered public accounting firm for the fiscal year ending December 31, 2026 and has further directed that management submit the selection of its independent registered public accounting firm for ratification by the stockholders at the Annual Meeting. Deloitte has audited our financial statements since 2021. Representatives of Deloitte are expected to be present at the Annual Meeting. They will have an opportunity to make a statement if they so desire and will be available to respond to appropriate questions.

Neither our Bylaws nor other governing documents or law require stockholder ratification of the selection of Deloitte as our independent registered public accounting firm. However, the Audit Committee of the Board is submitting the selection of Deloitte to the stockholders for ratification as a matter of good corporate practice. If the stockholders fail to ratify the selection, the Audit Committee of the Board will reconsider whether or not to retain that firm. Even if the selection is ratified, the Audit Committee of the Board in its discretion may direct the appointment of different independent auditors at any time during the year if they determine that such a change would be in our best interests and the best interests of our stockholders.

The affirmative vote of a majority of the votes cast on this matter, voting affirmatively or negatively (excluding abstentions and broker non-votes) will be required to ratify the selection of Deloitte.

Principal Accountant Fees and Services

The following table represents aggregate fees billed to us for the fiscal years ended December 31, 2025 and 2024, by Deloitte and its affiliates:

	Fiscal Year Ended December 31,
Fee Category	2025			2024
Audit fees(1)		$	891,805		$	1,509,739
Audit-related fees(2)			0			0
Tax fees(3)			64,800			32,400
All other fees(4)			1,895			1,895
Total fees		$	958,500		$	1,544,034

(1)

Audit fees consist of fees billed or expected to be billed for professional services provided in connection with the audit of our annual consolidated financial statements, the review of our quarterly condensed consolidated financial statements and audit services that are normally provided by the independent registered public accounting firm in connection with regulatory filings. For the fiscal year ended December 31, 2024, this category also included fees for services provided in connection with the IPO.

(2)

Audit-related fees consist of fees billed for assurance and related services that are reasonably related to the performance of the audit or review of our consolidated financial statements and not reported under “Audit Fees.”

(3)

Tax fees consist of fees for tax compliance, tax advice and tax planning services, including fees for professional services related to an Internal Revenue Code Section 382 study.

(4)

All other fees consist of aggregate fees billed for products and services provided by our independent registered public accounting firm other than those disclosed above and consist of fees for accessing Deloitte’s online accounting research tool.

Our Audit Committee was formed upon the consummation of our initial public offering (“IPO”). As a result, the Audit Committee did not pre-approve the portion of the foregoing services that occurred prior to our February 2024 IPO, although any services rendered prior to the formation of our Audit Committee were approved by our Board. All services performed and fees incurred subsequent to our IPO were pre-approved by our Audit Committee.

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Pre-Approval Policies and Procedures

The Audit Committee has adopted a policy and procedures for the pre-approval of audit and non-audit services rendered by our independent registered public accounting firm, Deloitte. The policy generally pre-approves specified services in the defined categories of audit services, audit-related services and tax services up to specified amounts. Pre-approval may also be given as part of the Audit Committee’s approval of the scope of the engagement of the independent auditor or on an individual, explicit, case-by-case basis before the independent auditor is engaged to provide each service. The pre-approval of services may be delegated to one or more of the Audit Committee’s members, but the decision must be reported to the full Audit Committee at its next scheduled meeting.

The Audit Committee has determined that the rendering of services other than audit services by Deloitte is compatible with maintaining the principal accountant’s independence.

THE BOARD OF DIRECTORS RECOMMENDS
A VOTE IN FAVOR OF PROPOSAL 2.

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PROPOSAL 3

APPROVAL OF AN AMENDMENT AND RESTATEMENT OF THE 2024 EQUITY
INCENTIVE PLAN

Overview

The Board is asking our stockholders to approve an amendment and restatement of the Alto Neuroscience, Inc. 2024 Equity Incentive Plan, which was approved by the Board on March 16, 2026, subject to approval of our stockholders at the Annual Meeting. In this proxy statement, we refer to the 2024 Equity Incentive Plan prior to the amendment and restatement as the “2024 Plan” and as amended and restated, the “Amended 2024 Plan.”

The 2024 Plan currently provides that the number of shares of common stock (“Common Stock”) reserved for issuance thereunder automatically increases on January 1 of each year by 5% of the number of shares of all classes of our Common Stock, regardless of the number of votes per share (“Capital Stock”), issued and outstanding on December 31 of the preceding calendar year, through calendar year 2034 (the “Evergreen Provision”), unless the Board determines to increase the share pool by a smaller number of shares.

The Amended 2024 Plan amends the Evergreen Provision such that the number of shares reserved for issuance under the Amended 2024 Plan will be automatically increased on January 1 of each year, beginning on January 1, 2027 and ending on and including January 1, 2034, by 5% of the sum of (i) the number of shares of Capital Stock issued and outstanding on December 31 of the preceding calendar year, and (ii) the number of shares of Capital Stock issuable upon the exercise of any pre-funded warrants outstanding as of December 31 of the preceding calendar year, unless the Board determines to increase the share pool by a smaller number of shares (the “Amended Evergreen Provision”). The Board has determined that it is in the best interests of the Company and our stockholders to seek stockholder approval of the Amended 2024 Plan, including the Amended Evergreen Provision, because, among other things, we have a continuing need to grant equity awards to attract and retain qualified personnel and to respond to relevant market changes in equity compensation practices.

If this Proposal 3 is approved by our stockholders, the Amended 2024 Plan will become effective as of the date of the Annual Meeting. In the event that our stockholders do not approve this Proposal 3, the Amended 2024 Plan will not become effective and the 2024 Plan will continue in its current form.

Summary of the Amended 2024 Plan

The following is a summary of the principal provisions of the Amended 2024 Plan. This summary, however, does not purport to be a complete description of all of the provisions of the Amended 2024 Plan and is qualified in its entirety by reference to the full text of the Amended 2024 Plan, which is attached as Appendix A to this proxy statement.

Types of Awards. Our Amended 2024 Plan provides for the grant of incentive stock options, or ISOs, to employees, including employees of any parent or subsidiary, and for the grant of nonstatutory stock options, or NSOs, stock appreciation rights, restricted stock awards, restricted stock unit awards, performance awards, and other forms of stock awards to employees, directors, and consultants, including employees and consultants of our affiliates. As of the Record Date, approximately 74 employees, five non-employee directors and six consultants would be eligible to participate in the Amended 2024 Plan.

Share Reserve. As of the Record Date, the maximum number of shares of Common Stock reserved for issuance pursuant to awards under the Amended 2024 Plan was 4,945,504 shares, of which up to 515,847 shares remained available for issuance. In addition, the Amended Evergreen Provision under the Amended 2024 Plan provides for an automatic increase in the number of shares reserved for issuance thereunder on January 1 of each calendar year from 2027 through 2034, equal to (a) 5% of the sum of (i) the number of shares of Capital Stock issued and outstanding on December 31 of the preceding calendar year, and (ii) the number of shares of Capital Stock issuable upon the exercise of any pre-funded warrants outstanding as of December 31 of the preceding calendar year or (b) a lesser amount as may be approved by the Board each year. The maximum number of shares of Common Stock that may be issued under the Amended 2024

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Plan pursuant to the exercise of options intended to qualify as ISOs within the meaning of Section 422 of the Internal Revenue Code of 1986, as amended (the “Code”), is 6,000,000 shares.

Shares subject to stock awards granted under our Amended 2024 Plan that expire or terminate without being exercised in full, or that are paid out in cash rather than in shares, do not reduce the number of shares available for issuance under our Amended 2024 Plan. Additionally, shares become available for future grant under our Amended 2024 Plan if they were issued under stock awards under our Amended 2024 Plan if we repurchase them or they are forfeited. This includes shares used to pay the exercise price of a stock award or to satisfy the tax withholding obligations related to a stock award.

Plan Administration. Our Board, or a duly authorized committee of our Board, will administer our Amended 2024 Plan. Our Board may also delegate to one or more persons or bodies the authority to do one or more of the following (i) designate recipients (other than officers) of specified stock awards provided that no person or body may be delegated authority to grant a stock award to themself; (ii) determine the number of shares subject to such stock award; and (iii) determine the terms of such stock awards. Under our Amended 2024 Plan, our Board has the authority to determine and amend the terms of awards and underlying agreements, including:

•

recipients;

•

the exercise, purchase or strike price of stock awards, if any;

•

the number of shares subject to such stock award;

•

the vesting schedule applicable to the awards, together with any vesting acceleration; and

•

the form of consideration, if any, payable on exercise or settlement of the award.

Under the Amended 2024 Plan, the Board also generally has the authority to effect, with the consent of any adversely affected participant:

•

the reduction of the exercise, purchase, or strike price of any outstanding award;

•

the cancellation of any outstanding award and the grant in substitution therefore of other awards, cash, or other consideration; or

•

any other action that is treated as a repricing under generally accepted accounting principles.

Stock Options. ISOs and NSOs are granted under stock option agreements adopted by the plan administrator. The plan administrator determines the exercise price for stock options, within the terms and conditions of the Amended 2024 Plan, provided that the exercise price of a stock option generally cannot be less than 100% of the fair market value of our Common Stock on the date of grant. Options granted under the Amended 2024 Plan vest at the rate specified in the stock option agreement as determined by the plan administrator.

Tax Limitations on ISOs. The aggregate fair market value, determined at the time of grant, of our Common Stock with respect to ISOs that are exercisable for the first time by an optionholder during any calendar year under all of our stock plans may not exceed $100,000. Options or portions thereof that exceed such limit will generally be treated as NSOs. No ISO may be granted to any person who, at the time of the grant, owns or is deemed to own stock possessing more than 10% of our total combined voting power or that of any of our affiliates unless (i) the option exercise price is at least 110% of the fair market value of the stock subject to the option on the date of grant; and (ii) the option is not exercisable after the expiration of five years from the date of grant.

Restricted Stock Unit Awards. Restricted stock units are granted under restricted stock unit award agreements adopted by the plan administrator. Restricted stock units may be granted in consideration for any form of legal consideration that may be acceptable to our Board and permissible under applicable law. A restricted stock unit may be settled by cash, delivery of stock, a combination of cash and stock as deemed appropriate by the plan administrator, or in any other form of consideration set forth in the restricted stock unit agreement. Additionally, dividend equivalents may be credited in respect of shares covered by a restricted stock unit. Except as otherwise provided in the applicable award agreement, restricted stock units that have not vested will be forfeited once the participant’s continuous service ends for any reason.

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Restricted Stock Awards. Restricted stock awards are granted under restricted stock award agreements adopted by the plan administrator. A restricted stock award may be awarded in consideration for cash, check, bank draft or money order, past services to us, or any other form of legal consideration that may be acceptable to our Board and permissible under applicable law. The plan administrator determines the terms and conditions of restricted stock awards, including vesting and forfeiture terms. If a participant’s service relationship with us ends for any reason, we may receive any or all of the shares of our Common Stock held by the participant that have not vested as of the date the participant terminates service with us through a forfeiture condition or a repurchase right.

Stock Appreciation Rights. Stock appreciation rights are granted under stock appreciation grant agreements adopted by the plan administrator. The plan administrator determines the purchase price or strike price for a stock appreciation right, which generally cannot be less than 100% of the fair market value of our Common Stock on the date of grant. A stock appreciation right granted under the Amended 2024 Plan vests at the rate specified in the stock appreciation right agreement as determined by the plan administrator.

Performance Awards. The Amended 2024 Plan permits the grant of performance-based stock and cash awards. The plan administrator may structure awards so that the shares of our stock, cash, or other property will be issued or paid only following the achievement of certain pre-established performance goals during a designated performance period. The performance criteria that will be used to establish such performance goals may be based on any measure of performance selected by the plan administrator. The performance goals may be based on a company-wide basis, with respect to one or more business units, divisions, affiliates, or business segments, and in either absolute terms or relative to the performance of one or more comparable companies or the performance of one or more relevant indices. Unless specified otherwise (i) in the award agreement at the time the award is granted or (ii) in such other document setting forth the performance goals at the time the goals are established, we will appropriately make adjustments in the method of calculating the attainment of performance goals as follows: (1) to exclude restructuring and/or other nonrecurring charges; (2) to exclude exchange rate effects; (3) to exclude the effects of changes to generally accepted accounting principles; (4) to exclude the effects of any statutory adjustments to corporate tax rates; (5) to exclude the effects of items that are “unusual” in nature or occur “infrequently” as determined under generally accepted accounting principles; (6) to exclude the dilutive effects of acquisitions or joint ventures; (7) to assume that any business divested by us achieved performance objectives at targeted levels during the balance of a performance period following such divestiture; (8) to exclude the effect of any change in the outstanding shares of our Common Stock by reason of any stock dividend or split, stock repurchase, reorganization, recapitalization, merger, consolidation, spin-off, combination or exchange of shares or other similar corporate change, or any distributions to Common Stockholders other than regular cash dividends; (9) to exclude the effects of stock based compensation and the award of bonuses under our bonus plans; (10) to exclude costs incurred in connection with potential acquisitions or divestitures that are required to be expensed under generally accepted accounting principles; (11) to exclude the goodwill and intangible asset impairment charges that are required to be recorded under generally accepted accounting principles; and (12) to exclude the effects of the timing of acceptance for review and/or approval of submissions to the FDA, EMA or other comparable regulatory authority. In addition, we retain the discretion to reduce or eliminate the compensation or economic benefit due upon attainment of the goals. The performance goals may differ from participant to participant and from award to award.

Other Stock Awards. The plan administrator may grant other awards based in whole or in part by reference to our Common Stock. The plan administrator will set the number of shares under the stock award and all other terms and conditions of such awards.

Non-Employee Director Compensation Limit. The aggregate value of all compensation granted or paid to any non-employee director with respect to any fiscal year, including stock awards granted and cash fees paid by us to such non-employee director, will not exceed $750,000 in total value, or in the event such non-employee director is first appointed or elected to the board during such fiscal year, $1,000,000 in total value (in each case, calculating the value of any such stock awards based on the grant date fair value of such stock awards for financial reporting purposes).

Changes to Capital Structure. In the event there is a specified type of change in our capital structure, such as a stock split, reverse stock split, or recapitalization, appropriate adjustments will be made to (i) the class and maximum number of shares reserved for issuance under the Amended 2024 Plan, (ii) the class and

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maximum number of shares by which the share reserve may increase automatically each year, (iii) the class and maximum number of shares that may be issued on the exercise of incentive stock options, and (iv) the class and number of shares and exercise price, strike price, or purchase price, if applicable, of all outstanding stock awards.

Corporate Transactions. The following applies to stock awards under the Amended 2024 Plan in the event of a corporate transaction, unless otherwise provided in a participant’s stock award agreement or other written agreement with us or one of our affiliates or unless otherwise expressly provided by the plan administrator at the time of grant.

In the event of a corporate transaction, any stock awards outstanding under the Amended 2024 Plan may be assumed, continued or substituted for by any surviving or acquiring corporation (or its parent company), and any reacquisition or repurchase rights held by us with respect to the stock award may be assigned to the successor (or its parent company). If the surviving or acquiring corporation (or its parent company) does not assume, continue or substitute for such stock awards, then with respect to any such stock awards that are held by participants whose continuous service has not terminated prior to the effective time of the transaction, or current participants, the vesting (and exercisability, if applicable) of such stock awards will be accelerated in full to a date prior to the effective time of the transaction (contingent upon the effectiveness of the transaction), and such stock awards will terminate if not exercised (if applicable) at or prior to the effective time of the transaction, and any reacquisition or repurchase rights held by us with respect to such stock awards will lapse (contingent upon the effectiveness of the transaction). With respect to performance awards with multiple vesting levels depending on performance level, unless otherwise provided by an award agreement or by the administrator, the award will accelerate at 100% of target. If the surviving or acquiring corporation (or its parent company) does not assume, continue or substitute for such stock awards, then with respect to any such stock awards that are held by persons other than current participants, such awards will terminate if not exercised (if applicable) prior to the effective time of the transaction, except that any reacquisition or repurchase rights held by us with respect to such stock awards will not terminate and may continue to be exercised notwithstanding the transaction. The plan administrator is not obligated to treat all stock awards or portions of stock awards in the same manner and is not obligated to take the same actions with respect to all participants.

In the event a stock award will terminate if not exercised prior to the effective time of a transaction, the plan administrator may provide, in its sole discretion, that the holder of such stock award may not exercise such stock award but instead will receive a payment equal in value to the excess (if any) of (i) the value of the property the participant would have received upon the exercise of the stock award over (ii) any exercise price payable by such holder in connection with such exercise.

Under our Amended 2024 Plan, a corporate transaction is defined to include: (i) a sale of all or substantially all of our assets; (ii) the sale or disposition of more than 50% of our outstanding securities; (iii) the consummation of a merger or consolidation where we do not survive the transaction; and (iv) the consummation of a merger or consolidation where we do survive the transaction but the shares of our Common Stock outstanding before such transaction are converted or exchanged into other property by virtue of the transaction, unless otherwise provided in an award agreement or other written agreement between us and the award holder. Under the Amended 2024 Plan, a change in control is defined to include (1) the acquisition by any person or company of more than 50% of the combined voting power of our then outstanding stock; (2) a merger, consolidation or similar transaction in which our stockholders immediately before the transaction do not own, directly or indirectly, more than 50% of the combined voting power of the surviving entity (or the parent of the surviving entity); (3) the approval by the stockholders or the Board of a plan of our complete dissolution or liquidation, or the occurrence of our complete dissolution or liquidation, except for a liquidation into a parent corporation; (4) a sale, lease, exclusive license or other disposition of all or substantially all of our assets other than to an entity more than 50% of the combined voting power of which is owned by our stockholders; and (5) an unapproved change in the majority of the Board.

Change in Control. In the event of a change in control, as defined under our Amended 2024 Plan, awards granted under our Amended 2024 Plan will not receive automatic acceleration of vesting and exercisability, although this treatment may be provided for in an award agreement.

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Clawback. All awards granted under the Amended 2024 Plan will be subject to recoupment in accordance with any clawback policy that we are required to adopt pursuant to the listing standards of any national securities exchange or association on which our securities are listed or as is otherwise required by the U.S. Dodd-Frank Wall Street Reform and Consumer Protection Act or other applicable law. In addition, our Board may impose such other clawback, recovery or recoupment provisions in a stock award agreement as our Board determines necessary or appropriate.

Transferability. A participant may not transfer stock awards under our Amended 2024 Plan other than by will, the laws of descent and distribution, or as otherwise provided under our Amended 2024 Plan.

Plan Amendment or Termination. Our Board has the authority to amend, suspend, or terminate our Amended 2024 Plan, provided that such action does not materially impair the existing rights of any participant without such participant’s written consent. Certain material amendments also require the approval of our stockholders. No incentive stock options may be granted after the tenth anniversary of the date our Board adopted our Amended 2024 Plan. No stock awards may be granted under our Amended 2024 Plan while it is suspended or after it is terminated.

Federal Income Tax Consequences

The following is a summary of the principal United States federal income tax consequences to participants and the Company with respect to participation in the Amended 2024 Plan. This summary is not intended to be exhaustive and does not discuss the income tax laws of any local, state or foreign jurisdiction in which a participant may reside. The information is based upon current federal income tax rules and therefore is subject to change when those rules change. Because the tax consequences to any participant may depend on his or her particular situation, each participant should consult the participant’s tax adviser regarding the federal, state, local and other tax consequences of the grant or exercise of an award or the disposition of shares acquired the Amended 2024 Plan. The Amended 2024 Plan is not qualified under the provisions of Section 401(a) of the Code, and is not subject to any of the provisions of the Employee Retirement Income Security Act of 1974, as amended. Our ability to realize the benefit of any tax deductions described below depends on our generation of taxable income as well as the requirement of reasonableness, the provisions of Section 162(m) of the Code, and the satisfaction of our tax reporting obligations.

Nonstatutory Stock Options

Generally, there is no taxation upon the grant of an NSO if the stock option is granted with an exercise price equal to the fair market value of the underlying shares on the grant date. Upon exercise, a participant will recognize ordinary income equal to the excess, if any, of the fair market value of the underlying shares on the date of exercise of the stock option over the exercise price. If the participant is employed by the Company or one of its affiliates, that income will be subject to withholding taxes. The participant’s tax basis in those shares will be equal to their fair market value on the date of exercise of the stock option, and the participant’s capital gain holding period for those shares will begin on that date.

We will generally be entitled to a tax deduction equal to the taxable ordinary income realized by the participant.

Incentive Stock Options

The Amended 2024 Plan provides for the grant of stock options that are intended to qualify as “incentive stock options,” as defined in Section 422 of the Code. Under the Code, a participant generally is not subject to ordinary income tax upon the grant or exercise of an ISO. If the participant holds a share received upon exercise of an ISO for more than two years from the date the stock option was granted and more than one year from the date the stock option was exercised, which is referred to as the required holding period, the difference, if any, between the amount realized on a sale or other taxable disposition of that share and the participant’s tax basis in that share will be long-term capital gain or loss.

If, however, a participant disposes of a share acquired upon exercise of an ISO before the end of the required holding period, which is referred to as a disqualifying disposition, the participant generally will recognize ordinary income in the year of the disqualifying disposition equal to the excess, if any, of the fair

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market value of the share on the date of exercise of the stock option over the exercise price. However, if the sales proceeds are less than the fair market value of the share on the date of exercise of the stock option, the amount of ordinary income recognized by the participant will not exceed the gain, if any, realized on the sale. If the amount realized on a disqualifying disposition exceeds the fair market value of the share on the date of exercise of the stock option, that excess will be short-term or long-term capital gain, depending on whether the holding period for the share exceeds one year.

For purposes of the alternative minimum tax, the amount by which the fair market value of a share acquired upon exercise of an ISO exceeds the exercise price of the stock option generally will be an adjustment included in the participant’s alternative minimum taxable income for the year in which the stock option is exercised. If, however, there is a disqualifying disposition of the share in the year in which the stock option is exercised, there will be no adjustment for alternative minimum tax purposes with respect to that share. In computing alternative minimum taxable income, the tax basis of a share acquired upon exercise of an ISO is increased by the amount of the adjustment taken into account with respect to that share for alternative minimum tax purposes in the year the stock option is exercised.

We are not allowed a tax deduction with respect to the grant or exercise of an ISO or the disposition of a share acquired upon exercise of an ISO after the required holding period. If there is a disqualifying disposition of a share, however, we will generally be entitled to a tax deduction equal to the taxable ordinary income realized by the participant, provided that either the employee includes that amount in income or we timely satisfy our reporting requirements with respect to that amount.

Restricted Stock Awards

Generally, the recipient of a restricted stock award will recognize ordinary income at the time the shares are received equal to the excess, if any, of the fair market value of the shares received over any amount paid by the recipient in exchange for the shares. If, however, the shares are not vested when they are received (for example, if the employee is required to work for a period of time in order to have the right to sell the shares), the recipient generally will not recognize income until the shares become vested, at which time the recipient will recognize ordinary income equal to the excess, if any, of the fair market value of the shares on the date they become vested over any amount paid by the recipient in exchange for the shares. A recipient may, however, file an election with the Internal Revenue Service, within 30 days following his or her receipt of the award, to recognize ordinary income, as of the date the recipient receives the award, equal to the excess, if any, of the fair market value of the shares on the date the award is granted over any amount paid by the recipient for the shares.

The recipient’s basis for the determination of gain or loss upon the subsequent disposition of shares acquired from a restricted stock award will be the amount paid for such shares plus any ordinary income recognized either when the shares are received or when the shares become vested.

We will generally be entitled to a tax deduction equal to the taxable ordinary income realized by the recipient of the restricted stock award.

Restricted Stock Unit Awards

Generally, the recipient of a restricted stock unit award structured to comply with the requirements of Section 409A of the Code or an exemption to Section 409A of the Code will recognize ordinary income at the time the shares are delivered equal to the excess, if any, of the fair market value of the shares received over any amount paid by the recipient in exchange for the shares. To comply with the requirements of Section 409A of the Code, the shares subject to a restricted stock unit award may generally only be delivered upon one of the following events: a fixed calendar date (or dates), separation from service, death, disability or a change in control. If delivery occurs on another date, unless the restricted stock unit award otherwise complies with or qualifies for an exemption to the requirements of Section 409A of the Code, in addition to the tax treatment described above, the recipient will owe an additional 20% federal tax and interest on any taxes owed.

The recipient’s basis for the determination of gain or loss upon the subsequent disposition of shares acquired from a restricted stock unit award will be the amount paid for such shares plus any ordinary income recognized when the shares are delivered.

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We will generally be entitled to a tax deduction equal to the taxable ordinary income realized by the recipient of the restricted stock unit award.

Stock Appreciation Rights

Generally, if a stock appreciation right is granted with an exercise price equal to the fair market value of the underlying shares on the grant date, the recipient will recognize ordinary income equal to the fair market value of the shares or cash received upon such exercise.

We will generally be entitled to a tax deduction equal to the taxable ordinary income realized by the recipient of the stock appreciation right.

Section 162(m) Limit

Under Section 162(m) of the Code (“Section 162(m)”), compensation paid to any publicly held corporation’s “covered employees” that exceeds $1 million per taxable year for any covered employee is generally non-deductible. Awards granted under the Amended 2024 Plan will be subject to the deduction limit under Section 162(m).

Common Stock Price

As of the record date, the closing price of a share of Common Stock on the New York Stock Exchange was $24.29.

New Plan Benefits under the Amended 2024 Plan

In general, awards to executive officers, other employees and consultants are made at the discretion of the administrator. As a result, the benefits and amounts that will be received or allocated to executive officers, other employees, and consultants under the Amended 2024 Plan are not determinable at this time. Pursuant to our non-employee director compensation policy (as amended effective November 11, 2025), each of our current non-employee directors would be eligible to receive an annual grant under the Amended 2024 Plan of an option to purchase the lesser of (1) 24,100 shares of Common Stock or (2) the largest whole number of shares of Common Stock that results in such option having an aggregate Black-Scholes value not exceeding $200,000. For more information regarding our non-employee director compensation policy, please see the section above entitled “Non-Employee Director Compensation”.

Aggregate Past Grants Under the 2024 Plan

As of the record date, awards covering a total of 5,108,876 shares of Common Stock have been granted under the 2024 Plan since its inception, inclusive of shares underlying awards that subsequently expired or were forfeited and became available for reissuance under the terms of the 2024 Plan. The following table shows information regarding the grant of such awards under the 2024 Plan (regardless of whether subsequently exercised or forfeited) to the persons and groups identified below.

Name and Position	Number of Options		Number of Restricted Stock Units
Amit Etkin, M.D., Ph.D., President, Chief Executive Officer, and Chair of the Board		744,000		34,711
Nicholas Smith, Chief Financial Officer and Chief Business Officer		425,000		19,153
Michael Hanley, Chief Operating Officer		452,000		0
All current executive officers as a group (4 persons)		1,894,000		53,864
All current non-employee directors as a group (5 persons)		308,190		0
All employees, including all current officers who are not executive officers, as a group		2,795,722		0

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Certain Interests of Directors

In considering the recommendation of our Board with respect to the approval of the Amended 2024 Plan, stockholders should be aware that the members of the Board have certain interests that may present them with conflicts of interest in connection with such proposal. As discussed above, directors are eligible to receive awards under the Amended 2024 Plan. The Board recognizes that approval of this proposal may benefit our directors and their successors.

Required Vote of Stockholders

Approval of Proposal 3 requires the affirmative vote of a majority of the votes cast on this proposal. Abstentions and broker non-votes are not considered votes cast and will have no effect on the outcome of Proposal 3.

THE BOARD OF DIRECTORS RECOMMENDS
A VOTE IN FAVOR OF PROPOSAL 3.

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PROPOSAL 4

APPROVAL OF AN AMENDMENT AND RESTATEMENT
OF THE 2024 EMPLOYEE STOCK PURCHASE PLAN

Overview

The Board is asking our stockholders to approve an amendment and restatement of the Alto Neuroscience, Inc. 2024 Employee Stock Purchase Plan, which was approved by the Board on March 16, 2026, subject to approval of our stockholders at the Annual Meeting. In this proxy statement, we refer to the 2024 Employee Stock Purchase Plan prior to the amendment and restatement as the “2024 ESPP” and as amended and restated, the “Amended 2024 ESPP.”

The 2024 ESPP currently provides that the number of shares of common stock (“Common Stock”) reserved for issuance thereunder automatically increases on January 1 of each year, commencing on January 1, 2025 and ending on (and including) January 1, 2034, in an amount equal to the lesser of (x) 1% of the number of shares of all classes of our Common Stock, regardless of the number of votes per share (“Capital Stock”), issued and outstanding on December 31 of the preceding calendar year, and (y) 750,000 shares of Common Stock (the “Evergreen Provision”), unless the Board determines to increase the share pool by a smaller number of shares.

The Amended 2024 ESPP amends the Evergreen Provision such that the number of shares reserved for issuance under the Amended 2024 ESPP will be automatically increased on January 1 of each year, beginning on January 1, 2027 and ending on (and including) January 1, 2034, by the lesser of (x) 1% of the sum of (i) the number of shares of Capital Stock issued and outstanding on December 31 of the preceding calendar year, and (ii) the number of shares of Capital Stock issuable upon the exercise of any pre-funded warrants outstanding as of December 31 of the preceding calendar year, or (y) 750,000 shares of Common Stock (the “Amended Evergreen Provision”). Approval of the Amended 2024 ESPP, including the Amended Evergreen Provision, will allow us to continue to provide our employees with the opportunity to acquire an ownership interest in the Company through their participation in the Amended 2024 ESPP, thereby encouraging them to remain in our service and more closely aligning their interests with those of our stockholders.

If this Proposal 4 is approved by our stockholders, the Amended 2024 ESPP will become effective as of the date of the Annual Meeting. In the event that our stockholders do not approve this Proposal 4, the Amended 2024 ESPP will not become effective and the 2024 ESPP will continue in its current form.

Summary of the Amended 2024 ESPP

The material features of the Amended 2024 ESPP are described below. The following description of the Amended 2024 ESPP is a summary only and is qualified in its entirety by reference to the complete text of the Amended 2024 ESPP. Stockholders are urged to read the actual text of the Amended 2024 ESPP in its entirety, which is attached as Appendix B to this proxy statement.

Purpose. The purpose of the Amended 2024 ESPP is to secure and retain the services of new employees, to retain the services of existing employees, and to provide incentives for such individuals to exert maximum efforts toward our success and that of our affiliates. Our Amended 2024 ESPP includes two components. One component is designed to allow eligible U.S. employees to purchase our ordinary shares in a manner that may qualify for favorable tax treatment under Section 423 of the Code. The other component permits the grant of purchase rights that do not qualify for such favorable tax treatment in order to allow deviations necessary to permit participation by eligible employees who are foreign nationals or employed outside of the U.S. while complying with applicable foreign laws.

Share Reserve. As of the record date, the maximum number of shares of Common Stock reserved for issuance under the 2024 ESPP was 839,100 shares. In addition, the Amended Evergreen Provision under the Amended 2024 ESPP provides for an automatic increase on January 1 of each calendar year, from 2027 through 2034, equal to the lesser of (i) 1% of the sum of (i) the number of shares of Capital Stock issued and outstanding on December 31 of the preceding calendar year, and (ii) the number of shares of Capital Stock issuable upon the exercise of any pre-funded warrants outstanding as of December 31 of the preceding calendar year, or (y) 750,000 shares of Common Stock; provided that before the date of any such increase,

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our Board may determine that such increase will be less than the amount set forth in clauses (i) and (ii). As of the record date, no offerings have commenced and no shares of our Common Stock have been purchased under the 2024 ESPP.

Administration. Our Board, or a duly authorized committee thereof, will administer our Amended 2024 ESPP. Our Board may delegate concurrent authority to administer the Amended 2024 ESPP to our Compensation and Management Development Committee under the terms of the Compensation and Management Development Committee’s charter. The Amended 2024 ESPP is implemented through a series of offerings under which eligible employees are granted purchase rights to purchase shares of our Common Stock on specified dates during such offerings. Under the Amended 2024 ESPP, we may specify offerings with durations of not more than 27 months and may specify shorter purchase periods within each offering. Each offering will have one or more purchase dates on which shares of our Common Stock will be purchased for employees participating in the offering. An offering under the Amended 2024 ESPP may be terminated under certain circumstances.

Payroll Deductions. Generally, all regular employees, including executive officers, employed by us or by any of our designated affiliates, may participate in the Amended 2024 ESPP and may contribute, normally through payroll deductions, up to 15% of their earnings (as defined in the Amended 2024 ESPP) for the purchase of our Common Stock under the Amended 2024 ESPP. Unless otherwise determined by our Board, Common Stock will be purchased for the accounts of employees participating in the Amended 2024 ESPP at a price per share that is at least the lesser of (i) 85% of the fair market value of a share of our Common Stock on the first date of an offering; or (ii) 85% of the fair market value of a share of our Common Stock on the date of purchase. As of the Record Date, approximately 73 employees were eligible to participate in the 2024 ESPP.

Limitations. Employees may have to satisfy one or more of the following service requirements before participating in the Amended 2024 ESPP, as determined by our Board, including: (i) customary employment with us or one of our affiliates for more than 20 hours per week and more than five months per calendar year; or (ii) continuous employment with us or one of our affiliates for a minimum period of time (not to exceed two years). No employee may purchase shares under the Amended 2024 ESPP at a rate in excess of $25,000 worth of our Common Stock based on the fair market value per share of our Common Stock at the beginning of an offering for each year such a purchase right is outstanding. Finally, no employee will be eligible for the grant of any purchase rights under the Amended 2024 ESPP if immediately after such rights are granted, such employee has voting power over 5% or more of our outstanding capital stock measured by vote or value under Section 424(d) of the Code.

Changes to Capital Structure. In the event that there occurs a change in our capital structure through such actions as a stock split, merger, consolidation, reorganization, recapitalization, reincorporation, stock dividend, dividend in property other than cash, large nonrecurring cash dividend, liquidating dividend, combination of shares, exchange of shares, change in corporate structure, or similar transaction, the Board will make appropriate adjustments to: (i) the number of shares reserved under the Amended 2024 ESPP; (ii) the maximum number of shares by which the share reserve may increase automatically each year; (iii) the number of shares and purchase price of all outstanding purchase rights; and (iv) the number of shares that are subject to purchase limits under ongoing offerings.

Corporate Transactions. In the event of certain significant corporate transactions, including: (i) a sale of all or substantially all of our assets; (ii) the sale or disposition of more than 50% of our outstanding securities; (iii) the consummation of a merger or consolidation where we do not survive the transaction; and (iv) the consummation of a merger or consolidation where we do survive the transaction but the shares of our Common Stock outstanding immediately before such transaction are converted or exchanged into other property by virtue of the transaction, any then-outstanding rights to purchase our stock under the Amended 2024 ESPP may be assumed, continued or substituted for by any surviving or acquiring entity (or its parent company). If the surviving or acquiring entity (or its parent company) elects not to assume, continue, or substitute for such purchase rights, then the participants’ accumulated payroll contributions will be used to purchase shares of our Common Stock within ten business days before such corporate transaction, and such purchase rights will terminate immediately.

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ESPP Amendment or Termination. Our Board has the authority to amend or terminate our Amended 2024 ESPP, provided that except in certain circumstances such amendment or termination may not materially impair any outstanding purchase rights without the holder’s consent. We will obtain stockholder approval of any amendment to our Amended 2024 ESPP as required by applicable law or listing requirements.

Federal Income Tax Information

The following is a summary of the principal United States federal income taxation consequences to participants and us with respect to participation in the Amended 2024 ESPP. This summary is not intended to be exhaustive and does not discuss the income tax laws of any local, state or foreign jurisdiction in which a participant may reside. The information is based upon current federal income tax rules and therefore is subject to change when those rules change. Because the tax consequences to any participant may depend on his or her particular situation, each participant should consult the participant’s tax adviser regarding the federal, state, local, and other tax consequences of the grant or exercise of a purchase right or the sale or other disposition of Common Stock acquired under the Amended 2024 ESPP. The Amended 2024 ESPP is not qualified under the provisions of Section 401(a) of the Internal Revenue Code and is not subject to any of the provisions of ERISA.

Rights granted under the Amended 2024 ESPP are intended to qualify for favorable federal income tax treatment associated with rights granted under an employee stock purchase plan which qualifies under the provisions of Section 423 of the Internal Revenue Code.

A participant will be taxed on amounts withheld for the purchase of shares of our Common Stock as if such amounts were actually received. Otherwise, no income will be taxable to a participant as a result of the granting or exercise of a purchase right until a sale or other disposition of the acquired shares. The taxation upon such sale or other disposition will depend upon the holding period of the acquired shares.

If the shares are sold or otherwise disposed of more than two years after the beginning of the offering period and more than one year after the shares are transferred to the participant, then the lesser of the following will be treated as ordinary income: (i) the excess of the fair market value of the shares at the time of such sale or other disposition over the purchase price; or (ii) the excess of the fair market value of the shares as of the beginning of the offering period over the purchase price (determined as of the beginning of the offering period). Any further gain or any loss will be taxed as a long-term capital gain or loss.

If the shares are sold or otherwise disposed of before the expiration of either of the holding periods described above, then the excess of the fair market value of the shares on the purchase date over the purchase price will be treated as ordinary income at the time of such sale or other disposition. The balance of any gain will be treated as capital gain. Even if the shares are later sold or otherwise disposed of for less than its fair market value on the purchase date, the same amount of ordinary income is attributed to the participant, and a capital loss is recognized equal to the difference between the sales price and the fair market value of the shares on such purchase date. Any capital gain or loss will be short-term or long-term, depending on how long the shares have been held.

There are no federal income tax consequences to us by reason of the grant or exercise of rights under the Amended 2024 ESPP. We are entitled to a deduction to the extent amounts are taxed as ordinary income to a participant for shares sold or otherwise disposed of before the expiration of the holding periods described above (subject to the requirement of reasonableness and the satisfaction of tax reporting obligations).

Common Stock Price

As of the record date, the closing price of a share of Common Stock on the New York Stock Exchange was $24.29.

New Plan Benefits under the Amended 2024 ESPP

Participation in the Amended 2024 ESPP is voluntary and each eligible employee will make his or her own decision regarding whether and to what extent to participate in the Amended 2024 ESPP. In addition, the Board and the Compensation and Management Development Committee have not granted any purchase rights under the Amended 2024 ESPP that are subject to stockholder approval of this Proposal 4. Accordingly,

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the benefits or amounts that will be received by or allocated to our executive officers and other employees under the Amended 2024 ESPP are not determinable. Our non-employee directors will not be eligible to participate in the Amended 2024 ESPP.

Plan Benefits under 2024 ESPP

As of the record date, no offerings have commenced and no shares of our Common Stock have been purchased under the 2024 ESPP.

Required Vote of Stockholders

Approval of Proposal 4 requires the affirmative vote of a majority of the votes cast on this proposal. Abstentions and broker non-votes are not considered votes cast and will have no effect on the outcome of Proposal 4.

THE BOARD OF DIRECTORS RECOMMENDS
A VOTE IN FAVOR OF PROPOSAL 4.

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EXECUTIVE OFFICERS

The following table sets forth information regarding our executive officers as of March 26, 2026. Each executive officer serves at the discretion of our Board and holds office until the executive officer’s successor is duly elected and qualified or until the executive officer’s earliest resignation or removal.

Name	Age	Position(s)
Amit Etkin, M.D., Ph.D.	49	President, Chief Executive Officer, and Chair of the Board
Nicholas Smith	37	Chief Financial Officer and Chief Business Officer
Michael Hanley	53	Chief Operating Officer
Adam Savitz, M.D., Ph.D.	60	Chief Medical Officer

Amit Etkin, M.D., Ph.D. Biographical information regarding Dr. Etkin is set forth under the section titled “Election of Directors—Continuing Directors” above.

Nicholas Smith has served as our Chief Financial Officer since November 2022 and has served as our Chief Business Officer since September 2021. Mr. Smith also served as a member of our board of directors from July 2023 through October 2023. Prior to joining us, Mr. Smith served in various roles at Aptinyx Inc., a CNS-focused biopharmaceutical company, from March 2017 until September 2021, including Vice President, Investor Relations and Corporate Development from March 2021 to September 2021, Senior Director, Corporate Development and Investor Relations from March 2019 to March 2021, and Director, Corporate Development from March 2017 to March 2019. Mr. Smith received a B.A. in Accounting and Finance from North Central College.

Michael Hanley has served as our Chief Operating Officer since May 2024. Prior to joining Alto, he served as Founder and Executive Director of Slainte Strategic Consulting LLC from May 2023 to May 2024. Mr. Hanley previously served as Chief Business Officer and Chief Commercial Officer of Aeglea BioTherapeutics, Inc. (“Aeglea”), a biotechnology company, from August 2022 to April 2023 and October 2019 to August 2022, respectively. Prior to Aeglea, Mr. Hanley served as Vice President and U.S. Chief Commercial Officer of Esteve Pharmaceuticals, S.A., a privately-held specialty pharmaceutical company, from April 2018 to September 2019. Mr. Hanley received a BBA in Marketing from the University of Notre Dame and an MBA from the Kellogg School of Management at Northwestern University.

Adam Savitz, M.D., Ph.D. has served as our Chief Medical Officer since July 2021. Before joining us, Dr. Savitz served in various roles at Janssen Research and Development, LLC, a pharmaceutical company, from May 2011 to June 2021, most recently serving as Senior Director Clinical Research from July 2017 to June 2021. From 2020 to 2021, he served as Clinical Strategy Leader for the Mood Disorder Disease Area Stronghold. Dr. Savitz completed his psychiatry training and served on the staff at Massachusetts General Hospital. He served as a full-time faculty member in the Department of Psychiatry at Weill Cornell Medicine, including as unit chief of an inpatient psychiatry unit, from 2001 until 2011. He received an M.D. and Ph.D. in Molecular Biology at the University of California, Los Angeles and a B.S./M.S. in Molecular Biophysics and Biochemistry from Yale University.

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SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

The following table sets forth information regarding beneficial ownership of our capital stock as of March 16, 2026 by:

•

each person, or group of affiliated persons, known by us to beneficially own more than 5% of our common stock;

•

each of our directors;

•

each of our named executive officers; and

•

all of our current executive officers and directors as a group.

We have determined beneficial ownership in accordance with the rules of the SEC, and the information is not necessarily indicative of beneficial ownership for any other purpose. These rules generally attribute beneficial ownership of securities to persons who possess sole or shared voting power or investment power with respect to those securities. Unless otherwise indicated, we believe based on information provided to us, the persons or entities identified in this table have sole voting and investment power with respect to all shares shown as beneficially owned by them, subject to applicable community property laws.

The percentage ownership information shown in the table below is based on 31,945,516 shares of common stock outstanding as of March 16, 2026. In computing the number of shares of common stock beneficially owned by a person and the percentage ownership of that person, we deemed to be outstanding all shares of common stock subject to stock options, warrants or other rights that are held by that person or entity that are either immediately exercisable or exercisable within 60 days of March 16, 2026. We did not deem these shares outstanding, however, for the purpose of computing the percentage ownership of any other person. Subsequent to March 16, 2026, and as previously reported on a Current Report on Form 8-K filed by us on March 16, 2026, we entered into a Securities Purchase Agreement with certain institutional investors (the “Purchasers”), pursuant to which we sold and issued to the Purchasers in a private placement transaction (i) 2,900,000 shares of our common stock, and (ii) with respect to certain Purchasers, pre-funded warrants to purchase 3,100,000 shares of our common stock (the “2026 Private Placement”). For purposes of the table presented below, the shares and pre-funded warrants issued in the 2026 Private Placement are not included.

Except as otherwise noted below, the address for each person or entity listed in the table is c/o Alto Neuroscience, Inc., 650 Castro Street, Suite 450, Mountain View, California 94041.

	Beneficial Ownership
Beneficial Owner	Number of Shares Beneficially Owned		Percentage of Shares Beneficially Owned
Greater than 5% Holders
Alpha Wave Ventures II, LP(1)		3,707,757		11.61%
Entities affiliated with Commodore Capital LP(2)		3,343,206		9.99%
Entities affiliated with Perceptive Advisors LLC(3)		3,347,512		9.99%
Entities affiliated with Point72 Asset Management(4)		2,824,275		8.69%
Vestal Point Capital LP(5)		2,485,000		7.78%
Amit Etkin, M.D., Ph.D.(6)		1,786,743		5.50%
Directors and Named Executive Officers:
Amit Etkin, M.D., Ph.D.(6)		1,786,743		5.50%
Nicholas Smith(7)		464,482		1.43%
Michael Hanley(8)		137,146		*
Christopher Nixon Cox(9)		785,527		2.45%
Andrew Dreyfus(10)		57,577		*
Husseini Manji, M.D.(11)		56,553		*
Raymond Sanchez, M.D.(12)		12,524		*
Gwill York(13)		131,048		*
All executive officers and directors as a group (9 persons)(14)		3,791,743		11.25%

Represents beneficial ownership of less than one percent.

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(1)

This information has been obtained from a Schedule 13G filed on February 8, 2024 by Alpha Wave Global, LP (“Alpha Wave”), Alpha Wave Ventures GP, Ltd. (“Alpha Wave Ventures GP”), Chimera Investment LLC (“Chimera”), and Lunate Holdings RSC LTD (“Lunate”). Consists of shares of common stock held by Alpha Wave Ventures II, LP. Alpha Wave Ventures GP, is the general partner of Alpha Wave Ventures II, LP, and therefore may be deemed to exercise voting and dispositive control over the shares held by Alpha Wave Ventures II, LP. Alpha Wave Ventures GP is a joint venture between Alpha Wave and Lunate. Lunate is a subsidiary of Chimera. Richard Gerson is the Chairman and Chief Investment Officer of Alpha Wave. Chimera is controlled by its board of directors. The address for each of Alpha Wave Ventures II, LP, Alpha Wave Ventures GP and Richard Gerson is 667 Madison Avenue, 19th Floor, New York, NY 10065. The address for Chimera is Office 410, Royal Group Headquarters Building, Khalifa Park Area, Abu Dhabi, United Arab Emirates. The address for Lunate is Unit No. 1, Floor 12, Al Maryah Tower, Abu Dhabi Global Market Square, Al Maryah Island, Abu Dhabi, United Arab Emirates.

(2)

This is based on the Company’s records and information obtained from a Schedule 13G/A filed on February 17, 2026 by Commodore Capital LP (“Commodore Capital”), Commodore Capital Master LP (“Commodore Master”), Robert Egen Atkinson, and Michael Kramarz. Consists of (i) 1,823,196 shares of common stock and (ii) 1,520,010 shares of common stock issuable upon the exercise of pre-funded warrants held by Commodore Master. Due to a beneficial ownership blocker in the pre-funded warrants, the number of shares beneficially owned excludes 16,344 shares of common stock issuable upon the exercise of pre-funded warrants held by Commodore Master. This does not include an additional (a) 900,000 shares and (b) pre-funded warrants to purchase 2,000,000 shares that we issued and sold to Commodore Master in the 2026 Private Placement. Commodore Capital is the investment manager to Commodore Master and may be deemed to beneficially own these securities. Michael Kramarz and Robert Egen Atkinson are the managing partners of Commodore Capital and exercise investment discretion with respect to these securities. The address for Commodore Capital, Robert Egen Atkinson, and Michael Kramarz is 444 Madison Avenue, Floor 35, New York, NY 10022. The address for Commodore Master is c/o Maples Corporate Services Limited, Ugland House, South Church Street, PO Box 309, Grand Cayman KY1-1103, Cayman Islands.

(3)

This is based on the Company’s records and information obtained from a Schedule 13G/A filed on February 17, 2026 by Perceptive Advisors LLC (“Perceptive Advisors”), Joseph Edelman, and Perceptive Life Sciences Master Fund. Ltd. (“Perceptive Master Fund”). Consists of (i) 1,784,393 shares of common stock and (ii) 1,563,119 shares of common stock issuable upon the exercise of pre-funded warrants held by Perceptive Master Fund. Due to a beneficial ownership blocker in the pre-funded warrants, the number of shares beneficially owned excludes 973,235 shares of common stock issuable upon the exercise of pre-funded warrants held by Perceptive Master Fund. Perceptive Advisors serves as the investment manager of Perceptive Master Fund. This does not include an additional (a) 362,500 shares and (b) pre-funded warrants to purchase 362,500 shares that we issued and sold to Perceptive Master Fund in the 2026 Private Placement. Joseph Edelman serves as the managing member of Perceptive Advisors. Accordingly, Perceptive Advisors and Mr. Edelman may be deemed to have beneficial ownership of the securities held of record by the Master Fund. Perceptive Advisors and Mr. Edelman do not own directly any shares of our common stock. The address for each of the entities and person listed above 51 Astor Place, 10th Floor, New York, NY 10003.

(4)

This is based on the Company’s records and information obtained from a Schedule 13G/A filed on February 17, 2026 by Point72 Asset Management, L.P. (“Point72 Asset Management”), Point72 Capital Advisors, Inc. (“Point72 Capital”), Point 72 Biotech Private Investments, LLC (“Point72 Biotech”), Differentiated Ventures Investments, LLC (“Differentiated Ventures”), 72 Investment Holdings, LLC (“72 Investment”), and Steven A. Cohen. Consists of (i) 1,606,954 shares of common stock and (ii) 549,543 shares of common stock issuable upon the exercise of pre-funded warrants held by Point72 Associates, LLC (“Point72 Associates”), and (iii) 667,778 shares of common stock held by Point72 Biotech. This does not include an additional (a) 237,500 shares and (b) pre-funded warrants to purchase 237,500 shares that we issued and sold to Point72 Associates in the 2026 Private Placement. Point72 Asset Management, Differentiated Ventures, and Mr. Cohen do not own directly any shares of our common stock. Pursuant to an investment management agreement, Point72 Asset Management maintains investment and voting power with respect to the securities held by Point72 Associates. Point72 Capital is the general partner of Point72 Asset Management. Mr. Cohen controls each of Point72

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Asset Management and Point72 Capital. Differentiated Ventures is the managing member of Point72 Biotech and may be deemed to share beneficial ownership over the shares of common stock held by Point72 Biotech. 72 Investment is the sole member of Differentiated Ventures and may be deemed to share beneficial ownership of the shares of common stock of which Differentiated Ventures may be deemed the beneficial owner. Mr. Cohen controls each of Point72 Biotech, Differentiated Ventures, and 72 Investment. The address for each of the entities and person listed above is 72 Cummings Point Road, Stamford, CT 06902.

(5)

This is based on the Company’s records and information obtained from a Schedule 13G filed on February 17, 2026 by Vestal Point Capital, LP (“Vestal”) and Ryan Wilder. Consists of 2,485,000 shares of common stock held by a certain fund and a managed account (the “Vestal Point Fund and Account”) of which Vestal is the investment adviser. This does not include an additional (a) 38,303 shares that we issued and sold to Vestal Point Master Fund, LP, in the 2026 Private Placement and (b) 36,697 shares that we issued and sold to an account associated with Vestal in the 2026 Private Placement. Mr. Wilder is the Chief Investment Officer and Managing Partner of Vestal and the Managing Member of Vestal Point Capital, LLC, the general partner of Vestal, with respect to the shares of common stock directly held by the Vestal Point Fund and Account. The address for each of the entities and person listed above is 632 Broadway, Suite 602, New York, NY 10012.

(6)

Consists of (a) 1,233,949 shares of common stock held by Dr. Etkin, and (b) 552,794 shares of common stock issuable upon the exercise of options held by Dr. Etkin that are exercisable within 60 days of March 16, 2026.

(7)

Consists of (a) 24,060 shares of common stock held by Mr. Smith, and (b) 440,422 shares of common stock issuable upon the exercise of options held by Mr. Smith that are exercisable within 60 days of March 16, 2026.

(8)

Consists of 137,146 shares of common stock issuable upon the exercise of options held by Mr. Hanley that are exercisable within 60 days of March 16, 2026.

(9)

Consists of (a) 715,653 shares of common stock held by Lightswitch Capital Fund I, L.P., or Lightswitch Capital, and (b) 69,874 shares of common stock issuable upon the exercise of options held by Mr. Cox that are exercisable within 60 days of March 16, 2026. Mr. Cox, a member of our board of directors, is the Chief Executive Officer of Lightswitch Capital GP, LLC, or Lightswitch GP, the general partner of Lightswitch Capital. As a result, each of Mr. Cox and Lightswitch GP may be deemed to have voting and investment power with respect to the shares held by Lightswitch Capital. The address for each of the entities and person listed above is 1133 Avenue of the Americas, New York, New York 10036.

(10)

Consists of 57,577 shares of common stock issuable upon the exercise of options held by Mr. Dreyfus that are exercisable within 60 days of March 16, 2026.

(11)

Consists of 56,553 shares of common stock issuable upon the exercise of options held by Dr. Manji that are exercisable within 60 days of March 16, 2026.

(12)

Consists of 12,524 shares of common stock issuable upon the exercise of options held by Dr. Sanchez that are exercisable within 60 days of March 16, 2026.

(13)

Consists of (a) 23,917 shares of common stock held by Ms. York and (b) 107,131 shares of common stock issuable upon the exercise of options held by Ms. York that are exercisable within 60 days of March 16, 2026.

(14)

Consists of (a) 2,037,430 shares of common stock held by our executive officers and directors, and (b) 1,754,313 shares of common stock issuable upon the exercise of options held by our executive officers and directors that are exercisable within 60 days of March 16, 2026.

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EXECUTIVE COMPENSATION

Summary Compensation Table

Our named executive officers for the year ended December 31, 2025, consisting of our principal executive officer and the next two most highly compensated executive officers who were serving in such capacity as of December 31, 2025, are:

•

Amit Etkin, M.D., Ph.D., our President, Chief Executive Officer, and Chair of the Board;

•

Nicholas Smith, our Chief Financial Officer and Chief Business Officer; and

•

Michael Hanley, our Chief Operating Officer.

The following table summarizes the total compensation of our named executive officers for their services performed in the years ended December 31, 2025 and 2024. This table should be read in conjunction with the “Narrative to the Summary Compensation Table” immediately below.

Name and Principal Position	Year		Salary ($)		Bonus ($)(1)		Stock Awards ($)(2)		Option Awards ($)(2)		Non-Equity Incentive Plan Compensation ($)		All Other Compensation ($)(3)		Total ($)
Amit Etkin, M.D., Ph.D. President, Chief Executive Officer, and Chair of the Board		2025		650,671		220,000		—		934,186		358,072		25,558		2,188,487
		2024		603,050		—		516,500		2,553,350		368,401		24,547		4,065,848
Nicholas Smith Chief Financial Officer and Chief Business Officer		2025		493,720		220,000		—		594,723		222,300		10,842		1,541,585
		2024		466,511		—		284,997		1,030,500		203,300		10,656		1,995,964
Michael Hanley Chief Operating Officer		2025		488,800		—		—		517,598		195,520		11,010		1,212,928
Michael Hanley Chief Operating Officer		2024		283,205		—		—		1,876,263		201,160		82,000		2,442,628

(1)

The amounts shown represent discretionary bonuses awarded to each of Dr. Etkin and Mr. Smith for 2025 in recognition of their respective efforts with regard to both our acquisition of assets from Chase Therapeutics Corporation and the $50 million private placement financing transaction completed in October 2025.

(2)

The amounts shown in the Stock Awards and Option Awards columns represent the grant date fair value of stock options and restricted stock units determined in accordance with Financial Accounting Standards Board Accounting Standards Codification, Topic 718. In addition, effective July 3, 2025, the Board approved a one-time repricing of certain stock options with exercise prices to have a per share exercise price of $2.35, subject to certain retention requirements, as described under “—Narrative to the Summary Compensation Table—Option Repricing,” below. With regard to the Option Awards, the amounts shown also include the incremental fair values of the option awards resulting from the Repricing. These amounts do not reflect dollar amounts actually received by the named executive officer or the economic value that may be received by the named executive officer upon stock option exercise or any sale of the underlying shares of common stock. The assumptions made in the valuation reflected in these columns are set forth in Note 11 to our Consolidated Financial Statements included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2025.

(3)

Amounts shown in the All Other Compensation column for 2025 are comprised of the following:

Company matching
contributions
under 401(k) plan

Term Life
Insurance
Premiums

SEC Form DEF 14A filed by Alto Neuroscience Inc.