<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0508</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2025-11-10</periodOfReport>

    <issuer>
        <issuerCik>0001984086</issuerCik>
        <issuerName>Septerna, Inc.</issuerName>
        <issuerTradingSymbol>SEPN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0002040349</rptOwnerCik>
            <rptOwnerName>Long Daniel D.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SEPTERNA, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>250 EAST GRAND AVENUE</rptOwnerStreet2>
            <rptOwnerCity>SOUTH SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94080</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>false</isDirector>
            <isOfficer>true</isOfficer>
            <isTenPercentOwner>false</isTenPercentOwner>
            <isOther>false</isOther>
            <officerTitle>SVP, Drug Discovery</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <aff10b5One>false</aff10b5One>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2025-11-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>3501</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>18.0586</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>92911</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The price reported in Column 4 is a weighted average price. The shares were sold in multiple transactions at prices ranging from $18.04 to $18.16. The Reporting Person undertakes to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares sold at each separate price within the range.</footnote>
        <footnote id="F2">Includes 3,501 shares acquired under the Septerna, Inc. 2024 Employee Stock Purchase Plan on October 31, 2025 in transactions that were exempt under Rule 16b-3(c).</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Ran Xiao, Attorney-in-Fact</signatureName>
        <signatureDate>2025-11-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
