DEF 14A

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 14A INFORMATION

Proxy Statement Pursuant to Section 14(a) of the

Securities Exchange Act of 1934

(Amendment No. )


Filed by the Registrant x	Filed by a party other than the Registrant o

Check the appropriate box:

o Preliminary Proxy Statement

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

x Definitive Proxy Statement

o Definitive Additional Materials

o Soliciting Material under § 240.14a-12

ATYR PHARMA, 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):

x No fee required

o Fee paid previously with preliminary materials

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

aTyr Pharma, Inc.

10240 Sorrento Valley Road, Suite #300

San Diego, CA 92121

NOTICE OF ANNUAL MEETING OF STOCKHOLDERS

To Be Held On May 11, 2026

Dear Stockholder:

You are cordially invited to attend the 2026 Annual Meeting of Stockholders (including any adjournments, continuations or postponements thereof, the “Annual Meeting”) of aTyr Pharma, Inc., a Delaware corporation (the “Company,” “we” or “us”). The Annual Meeting will be held on Monday, May 11, 2026 at 9:00 a.m. Pacific Time at the Company’s corporate headquarters located at 10240 Sorrento Valley Road, San Diego, CA 92121. The Annual Meeting is being held for the following purposes:

1. To elect three Class II directors, as nominated by the Company’s Board of Directors (the “Board of Directors”), to hold office until the 2029 annual meeting of stockholders or until their successors are duly elected and qualified;

2. To ratify the appointment of Ernst & Young LLP as the independent registered public accounting firm of the Company for its fiscal year ending December 31, 2026;

3. To approve, on an advisory basis, the compensation of the Company’s named executive officers;

4. To approve an amendment to the aTyr Pharma, Inc. 2015 Stock Option and Incentive Plan, as amended;

5. To approve an amendment to the Company’s Restated Certificate of Incorporation to increase the number of authorized shares of common stock from 170,000,000 to 340,000,000 shares; and

6. To transact such other business as may properly come before the Annual Meeting or any adjournment or postponement thereof.

These items of business are more fully described in the proxy statement for our Annual Meeting (“Proxy Statement”) accompanying this Notice of Annual Meeting of Stockholders. On or about March 26, 2026, we expect to mail to our stockholders a Notice of Internet Availability of Proxy Materials containing instructions on how to access our proxy materials, which include the Proxy Statement and our Annual Report on Form 10-K for the fiscal year ended December 31, 2025 (“Annual Report”), in lieu of mailing printed copies. The Notice of Internet Availability of Proxy Materials provides instructions on how to vote online or by telephone and how to request a paper copy of your proxy materials by mail.

Proposal 1 relates solely to the election of three Class II directors nominated by the Board of Directors and does not include any other matters relating to the election of directors, including without limitation, the election of directors nominated by any stockholder of the Company.

The Board of Directors has fixed the close of business on Monday, March 16, 2026 as the record date for the determination of stockholders entitled to notice of, and to vote at, the Annual Meeting.

All stockholders are cordially invited to attend the Annual Meeting. Whether or not you expect to attend the Annual Meeting in person, in order to ensure your representation at the Annual Meeting, you are requested to vote over the telephone or the internet as instructed in the Notice of Internet Availability of Proxy Materials that you will receive in the mail, or to complete, date, sign and return a proxy card if one is mailed to you. You may request a paper proxy card at any time on or before the Annual Meeting to submit your vote by mail; however, your shares will only be voted as directed in your proxy card if the proxy card is received by us prior to the Annual Meeting. If you attend the Annual Meeting and file with the Secretary of the Company an instrument revoking your proxy or a duly executed proxy bearing a later date, your proxy will not be used. Please note, however, that if your shares are held of record by a broker, bank or other nominee and you wish to vote at the meeting, you must obtain a proxy issued in your name from that record holder.


		By Order of the Board of Directors

		aTyr Pharma, Inc.


		Sanjay S. Shukla, M.D., M.S.
		President and Chief Executive Officer

San Diego, California
March 26, 2026

Your vote is important, whether or not you expect to attend the Annual Meeting in person. You are urged to vote either via the internet or telephone, or by mail by requesting a printed copy of the proxy card, as instructed in the Notice of Internet Availability of Proxy Materials that you will receive in the mail. Voting promptly will help avoid the additional expense of further solicitation to assure a quorum at the meeting.

TABLE OF CONTENTS


QUESTIONS AND ANSWERS ABOUT THESE PROXY MATERIALS AND VOTING		1
FORWARD-LOOKING STATEMENTS		6
PROPOSAL 1 - ELECTION OF DIRECTORS		7
PROPOSAL 2 - RATIFICATION OF THE INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM		15
PROPOSAL 3 - ADVISORY VOTE ON NAMED EXECUTIVE OFFICER COMPENSATION		16
PROPOSAL 4 - APPROVAL OF AN AMENDMENT TO THE 2015 STOCK OPTION AND INCENTIVE PLAN, AS AMENDED		17
PROPOSAL 5 - APPROVAL OF AN AMENDMENT TO THE COMPANY’S RESTATED CERTIFICATE OF INCORPORATION TO INCREASE THE NUMBER OF AUTHORIZED SHARES OF COMMON STOCK		23
EXECUTIVE OFFICERS		25
EXECUTIVE COMPENSATION		25
PAY VERSUS PERFORMANCE		37
DIRECTOR COMPENSATION		42
CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS		44
SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS		45
AUDIT COMMITTEE REPORT		47
STOCKHOLDER PROPOSALS FOR THE 2026 ANNUAL MEETING OF STOCKHOLDERS		48
HOUSEHOLDING OF PROXY MATERIALS		48
OTHER MATTERS		49

ATYR PHARMA, INC.

PROXY STATEMENT

FOR THE 2026 ANNUAL MEETING OF STOCKHOLDERS

To Be Held On May 11, 2026

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 is soliciting your proxy to vote at the 2026 Annual Meeting of Stockholders (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. Instructions on how to access the proxy materials over the internet or to request a printed copy may be found in the Notice.

We intend to mail the Notice on or about March 26, 2026 to all stockholders of record entitled to vote at the Annual Meeting.

Will I receive any other proxy materials by mail?

We may send you a proxy card, along with a second Notice, on or after April 5, 2026.

How do I attend the Annual Meeting?

The meeting will be held on Monday, May 11, 2026 at 9:00 a.m. Pacific Time at the Company’s corporate headquarters located at 10240 Sorrento Valley Road, San Diego, California 92121. Information on how to vote in person at the Annual Meeting is discussed below.

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 98,051,212 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 the Company’s transfer agent, Equiniti Trust Company, LLC, then you are a stockholder of record. As a stockholder of record, you may vote in person at the meeting or vote by proxy. Whether or not you plan to attend the meeting, we urge you to vote by proxy over the telephone or on the internet, or to fill out and return the proxy card that you may request or that we may elect to deliver at a later time to ensure your vote is counted.

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 should be 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 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 Annual 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 that you contact your broker, bank or other stockholder of record to do so.

What am I voting on?

There are five matters scheduled for a vote:

Election of three Class II directors (Proposal 1);

Ratification of selection of Ernst & Young LLP as independent registered public accounting firm of the Company for its fiscal year ending December 31, 2026 (Proposal 2);

Advisory approval of the compensation of the Company’s Named Executive Officers, as disclosed in this Proxy Statement in accordance with SEC rules (Proposal 3);

Approval of an amendment to the Company’s 2015 Stock Option and Incentive Plan, as amended (the “2015 Stock Plan”) (Proposal 4); and

Approval of an amendment to the Company’s Restated Certificate of Incorporation to increase the number of authorized shares of common stock from 170,000,000 to 340,000,000 shares (Proposal 5).

What if another matter is properly brought before the meeting?

The Board of Directors does not know of any other matters to be brought before the Annual Meeting. If any other matters are presented, the proxy holders have discretionary authority to vote all proxies in accordance with their best judgment. Discretionary authority for them to do so is provided for in the proxy card.

How do I vote?

For proposal 1, you may either vote “FOR” all the nominees to the Board of Directors or you may “WITHHOLD” your vote for any nominee to the Board of Directors that you specify. For each of the other matters to be voted on, you may vote “FOR,” “AGAINST” or “ABSTAIN.”

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 you may vote by proxy over the telephone, or through the internet or using a proxy card that you may request or that we may elect to deliver at a later time. 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 Annual Meeting and vote at the Annual Meeting even if you have already voted by proxy. This is only required if you want to change your original vote, since votes will not be double counted.

(1)

To vote in person, come to the Annual Meeting and we will give you a ballot when you arrive.

(2)

To vote prior to the Annual Meeting (until 11:59 p.m. Eastern Time on May 10, 2026) you may vote via the internet at https://web.viewproxy.com/atyr/2026; by telephone; or by completing and returning the proxy card or voting instruction form, as described below.

To vote over the telephone, dial toll-free 1-866-402-3905 using a touch-tone phone and follow the recorded instructions. You will be asked to provide the control number from the Notice or proxy card. Your telephone vote must be received by 11:59 p.m. Eastern Time on May 10, 2026 to be counted.

ii.

To vote through the internet prior to the meeting, go to https://web.viewproxy.com/atyr/2026 and follow the instructions to submit your vote on an electronic proxy card. You will be asked to provide the control number from the Notice or proxy card. Your internet vote must be received by 11:59 p.m. Eastern Time on May 10, 2026 to be counted.

iii.

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

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 Notice containing voting instructions from that organization rather than from the Company. You must follow these instructions 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 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.

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.

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 telephone, through the internet, by completing your proxy card or in person 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” (i) the election of each of the Company’s three nominees as directors; (ii) the ratification of the appointment of Ernst & Young LLP as the independent registered public accounting firm for the Company for the fiscal year ending December 31, 2026; (iii) the advisory approval of the compensation of the Company’s Named Executive Officers; (iv) the amendment to the 2015 Stock Plan; (v) the amendment to the Company’s Restated Certificate of Incorporation to increase the number of authorized shares of common stock from 170,000,000 to 340,000,000 shares; and (vi) as the proxy holders deem advisable, in their discretion, on other matters that may properly come before the Annual Meeting.

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 (“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. In this regard, the NYSE has advised us that Proposals 1, 3 and 4 are considered “non-routine” matters under NYSE rules, meaning that we expect your broker may not vote your shares on those proposals in the absence of your voting instructions. However, the NYSE has advised us that Proposals 2 and 5 are considered “routine” matters under NYSE rules meaning that if you do not return voting instructions to your broker by its deadline, we expect that your shares may be voted by your broker in its discretion on Proposals 2 and 5.

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.

What are “broker non-votes”?

As discussed above, when a beneficial owner of shares held in street name does not give voting instructions to his or her broker, bank or other securities intermediary holding his or her shares as to how to vote on matters deemed to be “non-routine,” the broker, bank or other such agent cannot vote the shares. When there is at least one “routine” matter that the broker, bank or other securities intermediary votes on, the shares that are un-voted on “non-routine” matters are counted as “broker non-votes.” The NYSE has advised us that Proposals 2 and 5 are considered “routine” matters and we therefore do not expect there to be any broker non-votes on this proposal. The NYSE has advised us that Proposals 1, 3 and 4 are considered “non-routine” matters and we therefore expect broker non-votes to exist in connection with these proposals.

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.

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 and Alliance Advisors, LLC (“Alliance Advisors”) may also solicit proxies in person, by email, by telephone, or by other means of communication. Directors and employees will not be paid any additional compensation for soliciting proxies, but Alliance Advisors will be paid its customary fee, which is not expected to exceed $17,000. We will 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 the 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 Annual Meeting. If you are the record holder of your shares, you may revoke your proxy in any one of the following ways:

(1)

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

(2)

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

(3)

You may send a timely written notice that you are revoking your proxy to the Company’s Secretary at 10240 Sorrento Valley Road, Suite #300, San Diego, CA 92121. Such notice will be considered timely if it is received at the indicated address by the close of business on the business day one week preceding the date of the Annual Meeting.

(4)

You may attend the Annual Meeting and vote in person. Simply attending the Annual Meeting will not, by itself, revoke your proxy.

Your most current telephone or internet proxy or proxy card 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 by your broker, bank or other agent.

How are votes counted?

To elect our directors and approve the other proposals being considered at the Annual Meeting, the voting requirements are as follows:


Proposal	Vote Required	Discretionary Voting Permitted?
1. Election of Directors	Plurality	No
2. Ratification of Ernst & Young LLP

SEC Form DEF 14A filed by aTyr Pharma Inc.