
BridgeBio Oncology Therapeutics, Inc.63,054,549 Shares of Common Stock by the Selling Securityholders This prospectus supplement no. 3 (this “Prospectus Supplement”) amends and supplements the prospectus dated September 10,2025 (as may be supplemented or amended from time to time, the “Prospectus”), which forms part of our Registration Statement onForm S-1 (Registration Statement No. 333-289940). This Prospectus Supplement is being filed to update and supplement theinformation included or incorporated by reference in the Prospectus with the information contained in the attached Annual Reporton Form 10-K, filed with the Securities and Exchange Commission (the “Securities and Exchange Commission”) on March 5, 2026(the “Form 10-K”). Accordingly, we have attached the Form 10-K to this Prospectus Supplement. This Prospectus Supplement updates and supplements the information in the Prospectus and is not complete without, and may notbe delivered or utilized except in combination with, the Prospectus, including any amendments or supplements thereto. ThisProspectus Supplement should be read in conjunction with the Prospectus, and if there is any inconsistency between theinformation in the Prospectus and this Prospectus Supplement, you should rely on this Prospectus Supplement. Our common stock, par value $0.0001 per share (“Common Stock”) is listed on Nasdaq Global Market (“Nasdaq”) under thesymbol “BBOT”. On March 5, 2026, the closing price of our Common Stock as reported on Nasdaq was $9.89 per share. We are an “emerging growth company” as that term is defined under the federal securities laws and, as such, are subject tocertain reduced public company reporting requirements. Investing in our securities involves risks that are described in the “Risk Factors” section beginning on page 42 of the Form10-K. Neither the SEC nor any state securities commission has approved or disapproved of the securities to be issued under thisprospectus or determined if this prospectus is truthful or complete. Any representation to the contrary is a criminal offense. The date of this Prospectus Supplement is March 6, 2026. wUNITED STATESSECURITIES AND EXCHANGE COMMISSIONWashington, D.C. 20549FORM 10-K (Mark One) ☒ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934For the fiscal year ended December 31, 2025OR☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THETRANSITION PERIOD FROMTOCommission File Number 001-41955 BRIDGEBIO ONCOLOGY THERAPEUTICS, INC. (Exact name of Registrant as specified in its Charter) Securities registered pursuant to Section 12(b) of the Act: Securities registered pursuant to Section 12(g) of the Act:None Indicate by check mark if the Registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. YES☐NO☒ Indicate by check mark if the Registrant is not required to file reports pursuant to Section 13 or 15(d) of the Act. YES☐NO☒ Indicate by check mark whether the Registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during thepreceding 12 months (or for such shorter period that the Registrant was required to file such reports), and (2) has been subject to such filing requirements for the past90 days. YES☒NO☐ Indicate by check mark whether the Registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of RegulationS-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the Registrant was required to submit such files). YES☒NO☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, or an emerginggrowth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2of the Exchange Act. Large accelerated filer☐Non-accelerated filer☒Emerging growth company☒ Accelerated filer Smaller reporting company If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revisedfinancial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐ Indicate by check mark whether the registrant has filed a report on and attestation to its management’s assessment of the effectiveness of its internal control overfinancial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm that prepared or issued its auditreport.☐If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in the filing reflect the correction of an error to previously issued financial statements.☐ Indicate by check mark whether any of those




