Aprea Therapeutics, Inc.

Our Annual Report on Form 10-K for the fiscal year ended December 31, 2024, including the consolidated financial statements, has been filed with the SEC and provides additional information about us. It is available on our corporate website at www.aprea.com and you may request a paper copy (excluding exhibits) without charge upon written request to Chief Financial Officer, Aprea Therapeutics, Inc., 3805 Old Easton Road, Doylestown, PA 18902. In addition, our 2024 Annual Report on Form 10-K is available to registered holders of our common stock atwww.proxyvote.com.

Signature [PLEASE SIGN WITHIN BOX] Date Signature (Joint Owners) Date TO VOTE, MARK BLOCKS BELOW IN BLUE OR BLACK INK AS FOLLOWS: KEEP THIS PORTION FOR YOUR RECORDS DETACH AND RETURN THIS PORTION ONLY THIS PROXY CARD IS VALID ONLY WHEN SIGNED AND DATED. V66377-P27837 ! ! ! For All Withhold All For All Except For Against Abstain ! ! ! ! ! ! To withhold authority to vote for any individual nominee(s), mark "For All Except" and write the number(s) of the nominee(s) on the line below. APREA THERAPEUTICS, INC. 1. ELECTION OF THREE CLASS III DIRECTORS The Board of Directors recommend a vote FOR all the nominees listed in Proposal 1 and FOR Proposals 2 and 3. The Board of Directors recommends you vote 1 Year on the following proposal: Please sign exactly as name(s) appear(s) hereon. Joint owners should each sign. When signing as attorney, executor, administrator, corporate officer, trustee, guardian, or custodian, please give full title. 01) Jean-Pierre Bizzari, M.D. 02) Oren Gilad, Ph.D. 03) John B. Henneman III 2. To ratify the appointment of EisnerAmper LLP as our independent registered public accounting firm for fiscal year 2025. 3. To approve, by non-binding advisory vote, the compensation of our named executive officers. 4. To approve, by non-binding advisory vote, the frequency of future votes on the compensation of our named executive officers. ! ! ! ! 1 Year 2 Years 3 Years Abstain SCAN TO VIEW MATERIALS & VOTEw APREA THERAPEUTICS, INC. 3805 OLD EASTON ROAD DOYLESTOWN, PA 18902 VOTE BY INTERNET Before The Meeting - Go to www.proxyvote.com or scan the QR Barcode above Use the Internet to transmit your voting instructions and for electronic delivery of information up until 11:59 p.m. Eastern Time the day before the cut-off date or meeting date. Have your proxy card in hand when you access the web site and follow the instructions to obtain your records and to create an electronic voting instruction form. During The Meeting - Go to www.virtualshareholdermeeting.com/APRE2025 You may attend the meeting via the Internet and vote during the meeting. Have the information that is printed in the box marked by the arrow available and follow the instructions. VOTE BY PHONE - 1-800-690-6903 Use any touch-tone telephone to transmit your voting instructions up until 11:59 p.m. Eastern Time the day before the cut-off date or meeting date. Have your proxy card in hand when you call and then follow the instructions. VOTE BY MAIL Mark, sign and date your proxy card and return it in the postage-paid envelope we have provided or return it to Vote Processing, c/o Broadridge, 51 Mercedes Way, Edgewood, NY 11717.

V66378-P27837 Important notice regarding the internet availability of proxy materials for the Annual Meeting of Stockholders. The Notice and Proxy Statement and Form 10-K are available at www.proxyvote.com Small steps make an impact. Help the environment by consenting to receive electronic delivery, sign up at www.envisionreports.com/APRE The 2025 Annual Meeting of Stockholders of Aprea Therapeutics, Inc. will be held on Thursday, June 5, 2025, 9:00 A.M. Eastern Time, virtually via the internet at www.virtualshareholdermeeting.com/APRE2025 To access the virtual meeting, you must have the information that is printed in the shaded bar located on the reverse side of this form. Proxy – APREA THERAPEUTICS, INC. 2025 Annual Meeting of Stockholders Proxy Solicited by Board of Directors for Annual Meeting – June 5, 2025 Oren Gilad, Ph.D. and John P. Hamill, or any of them, each with the power of substitution, are hereby authorized to represent and vote the shares of the undersigned, with all the powers which the undersigned would possess if personally present, at the Annual Meeting of Stockholders of Aprea Therapeutics, Inc. to be held on June 5, 2025, or at any postponement or adjournment thereof. Shares represented by this proxy will be voted as directed by the stockholder. If no such direction is made, this proxy will be voted in accordance with the Board of Directors' recommendations. In their discretion, the proxies are authorized to vote upon such other business as may properly come before the meeting. (Continued and to be signed on the reverse side)