Upstream Bio Inc IPO prospectus (as of 2026-03-26 version)

PROSPECTUS SUPPLEMENT(To prospectus dated November5, 2025) Up to $150,000,000 Common Stock We have entered into a Sales Agreement (the “sales agreement”) with Leerink Partners LLC (the “sales agent”), dated March26, 2026, relating tothe sale of shares of our common stock, par value $0.001 per share (“common stock”). In accordance with the terms of the sales agreement, pursuant tothis prospectus supplement and the accompanying prospectus, we may offer and sell shares of our common stock having an aggregate offering price of Our common stock is listed on The Nasdaq Global Select Market under the symbol “UPB.” On March24, 2026, the last reported sale price of ourcommon stock on The Nasdaq Global Select Market was $8.45 per share. Sales of our common stock, if any, under this prospectus supplement will be made by any method permitted that is deemed to be an “at the marketoffering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended (the “Securities Act”). The sales agent is not requiredto sell any specific number or dollar amount of securities, but will act as a sales agent using commercially reasonable efforts consistent with its normal The sales agent will be entitled to compensation under the terms of the sales agreement at a commission rate of up to 3.0% of the gross proceedsof any shares of our common stock sold under the sales agreement. In connection with the sale of our common stock on our behalf, the sales agent willbe deemed to be an “underwriter” within the meaning of the Securities Act and the compensation of the sales agent will be deemed to be underwriting We are an “emerging growth company” and a “smaller reporting company” under the federal securities laws and, as such, we have elected tocomply with certain reduced public company reporting requirements for this prospectus supplement and for future filings. See “Prospectus Supplement Investing in our common stock involves a high degree of risk. See “Risk Factors” beginning on page S-5 of thisprospectus supplement and page 1 of the accompanying prospectus, and under similar headings in the other documentsthat are incorporated by reference into this prospectus supplement and the accompanying prospectus for a discussionof the factors you should carefully consider before deciding to purchase our common stock. Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities, orpassed upon the adequacy or accuracy of this prospectus supplement or the accompanying prospectus. Any representation to the contrary is acriminal offense. Leerink Partners The date of this prospectus supplement is March26, 2026. TABLE OF CONTENTS ABOUT THIS PROSPECTUSRISK FACTORSSPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS Table of Contents ABOUT THIS PROSPECTUS SUPPLEMENT This prospectus supplement is part of an automatic shelf registration statement on Form S-3 (File No.333-291267) that we filed with theSecurities and Exchange Commission (the “SEC”) on November5, 2025, as a “well-known seasoned issuer” as defined in Rule 405 of the SecuritiesAct using a “shelf” registration process, and consists of two parts. The first part is this prospectus supplement, including the documents incorporated byreference herein, which describes the specific terms of this offering. The second part, the accompanying prospectus, including the documentsincorporated by reference therein, gives more general information, some of which may not apply to this offering. Generally, when we refer to the“prospectus,” we are referring to both parts combined. This prospectus supplement and any free writing prospectus we authorize for use in connection You should rely only on the information contained in or incorporated by reference into this prospectus supplement and the accompanyingprospectus, along with the information contained in any free writing prospectus that we have authorized for use in connection with this offering. Wehave not, and the sales agent has not, authorized anyone to provide you with different or additional information. If anyone provides you with different orinconsistent information, you should not rely on it. We and the sales agent take no responsibility for, and can provide no assurance as to the reliability of,any other information that others may give you. You should assume that the information appearing in this prospectus supplement, the accompanyingprospectus, the documents incorporated by reference in this prospectus supplement and the accompanying prospectus, and in any free writing prospectusthat we have authorized for use in connection with this offering is accurate only as of the respective dates of those documents, unless we indicate We further note that the representations, warranties and covenants made by us in any agreement that is filed as an exhibit to any document that isincorporated by reference herein were made solely for the benefit of the parties