SCHEDULE 13D/A 0000902664-24-005639 0001998597 XXXXXXXX LIVE 2 Common Stock, par value $0.01 per share 03/11/2025 false 0001560327 753422104 Rapid7, Inc.

120 CAUSEWAY STREET BOSTON MA 02114

Ele Klein & Adriana Schwartz 212-756-2000 Schulte Roth & Zabel LLP 919 Third Avenue New York NY 10022 0001998597 N JANA PARTNERS MANAGEMENT, LP a AF N DE 3690129.00 0.00 3690129.00 0.00 3690129.00 N 5.8 IA PN Y MICHAEL JOSEPH BURNS a PF N X1 3000.00 0.00 3000.00 0.00 3000.00 N 0.0 IN 0001213097 N ROBERT BRADSHAW HENSKE a PF N X1 1500.00 0.00 1500.00 0.00 1500.00 N 0.0 IN Y CHAD KINZELBERG a PF N X1 3000.00 0.00 3000.00 0.00 3000.00 N 0.0 IN Common Stock, par value $0.01 per share Rapid7, Inc. 120 CAUSEWAY STREET BOSTON MA 02114 This Amendment No. 2 ("Amendment No. 2") amends the statement on Schedule 13D filed with the Securities and Exchange Commission (the "SEC") on September 27, 2024 (as amended from time to time, the "Schedule 13D") with respect to the Shares of the Issuer. This Amendment No. 2 amends Items 4, 6, and 7 as set forth below. Capitalized terms used herein and not otherwise defined in this Amendment No. 2 have the meanings set forth in the Schedule 13D. Item 4 is hereby amended and supplemented with the addition of the following: On March 11, 2025, JANA entered into nominee agreements (the "Nominee Agreements") with each of Michael Joseph Burns and Chad Kinzelberg (each, a "Nominee" and collectively, the "Nominees"), which is further described in the Reporting Persons' response to Item 6 of this Amendment No. 2, which is incorporated by reference into this Item 4. Item 6 is hereby amended and supplemented with the addition of the following: On March 11, 2025, JANA entered into Nominee Agreements with each of the Nominees pursuant to which each Nominee has agreed, upon the election of JANA, to become members of a slate of nominees and to stand for election as directors of the Issuer at the 2025 Annual Meeting. Pursuant to the Nominee Agreements, JANA has agreed to pay the costs of soliciting proxies in connection with the 2025 Annual Meeting, and to defend and indemnity the Nominees against, and with respect to, any losses that may be incurred by the Nominees in the event they become party to litigation based on their nomination as candidates for election to the Board and the solicitation of proxies in support of their election. Each of the Nominees received compensation under their respective Nominee Agreement in the amount of $50,000, and each will receive an additional $150,000 in the event of his election to the Board in a contested election. Each of the Nominees agreed, if elected to the Board, to hold Shares with a market value equal to $200,000 (adjusted for taxes) as of the date of his election (subject to certain exceptions), until the later of when he is no longer a director of the Issuer and three years (subject to certain exceptions). The foregoing summary of the Nominee Agreements is not complete and is qualified in its entirety by reference to the full text of the form of Nominee Agreement, a copy of which is attached as Exhibit 99.2 hereto and is incorporated by reference herein. Exhibit 99.2: Form of Nominee Agreement JANA PARTNERS MANAGEMENT, LP /s/ Jennifer Fanjiang 03/13/2025 MICHAEL JOSEPH BURNS /s/ Michael Joseph Burns 03/13/2025 ROBERT BRADSHAW HENSKE /s/ Robert Bradshaw Henske 03/13/2025 CHAD KINZELBERG /s/ Chad Kinzelberg 03/13/2025