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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2021-04-01</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001807901</issuerCik>
        <issuerName>Pandion Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>PAND</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001171002</rptOwnerCik>
            <rptOwnerName>BELOFF GREGG</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O PANDION THERAPEUTICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>134 COOLIDGE AVENUE</rptOwnerStreet2>
            <rptOwnerCity>WATERTOWN</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02472</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2021-04-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>U</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>13196</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>60.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Danforth Advisors, LLC</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Pursuant to the Agreement and Plan of Merger (the &quot;Merger Agreement&quot;), dated February 24, 2021, among Pandion Therapeutics, Inc. (the &quot;Company&quot;), Merck Sharp &amp; Dohme Corp. (&quot;Merck&quot;) and Panama Merger Sub, Inc. (&quot;Merger Sub&quot;), Merger Sub commenced a tender offer (the &quot;Offer&quot;) to purchase all outstanding Company common stock for the price of $60.00 per share in cash (the &quot;Offer Price&quot;). On April 1, 2021, the Offer consummated, after which Merger Sub merged with and into the Company (the &quot;Merger&quot;) and the Company became a wholly owned subsidiary of Merck. At the consummation of the Offer and the Merger, respectively, (i) Merger Sub purchased all shares of Company common stock that were validly tendered pursuant to the Offer for a cash payment equal to the Offer Price and (ii) all shares of Company common stock outstanding immediately prior to the effective time of the Merger (the &quot;Effective Time&quot;), were cancelled and converted automatically into the right to receive the Offer Price.</footnote>
    </footnotes>

    <remarks>Interim Chief Financial Officer</remarks>

    <ownerSignature>
        <signatureName>/s/ Edward D. Freedman, as attorney-in-fact for Gregg Beloff</signatureName>
        <signatureDate>2021-04-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
