<?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>0001598542</rptOwnerCik>
            <rptOwnerName>Carroll Jill</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>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </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>5674221</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>See footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Employee Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>18.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2021-04-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>13997</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2030-07-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>13997</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <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>
        <footnote id="F2">The shares reported herein are held of record by S.R. One, Limited, an indirect, wholly-owned subsidiary of GlaxoSmithKline plc. As Principal at S.R. One, Limited and an employee of GlaxoSmithKline LLC, Ms. Carroll disclaims beneficial ownership of all the shares held by S.R. One, Limited and this report shall not be deemed an admission of beneficial ownership of such shares for the purposes of Section 16 or for any other purpose except to the extent of her pecuniary interest therein.</footnote>
        <footnote id="F3">All options were vested and exercisable as of immediately prior to the Effective Time.</footnote>
        <footnote id="F4">Disposed of pursuant to the Merger Agreement in exchange for the excess of the Offer Price over the exercise price of the option.</footnote>
    </footnotes>

    <remarks></remarks>

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