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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2020-08-18</periodOfReport>

    <dateOfOriginalSubmission>2020-08-18</dateOfOriginalSubmission>

    <noSecuritiesOwned>1</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001802665</issuerCik>
        <issuerName>Harmony Biosciences Holdings, Inc.</issuerName>
        <issuerTradingSymbol>HRMY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001602402</rptOwnerCik>
            <rptOwnerName>Nielsen Jack</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O HARMONY BIOSCIENCES, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>630 W. GERMANTOWN PIKE, SUITE 215</rptOwnerStreet2>
            <rptOwnerCity>PLYMOUTH MEETING</rptOwnerCity>
            <rptOwnerState>PA</rptOwnerState>
            <rptOwnerZipCode>19462</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <footnotes></footnotes>

    <remarks>Due to an administrative error, the original Form 3 reported shares that the Reporting Person does not beneficially own.</remarks>

    <ownerSignature>
        <signatureName>/s/ Stephanie Wisdo, Attorney-in-fact for Jack Bech Nielsen</signatureName>
        <signatureDate>2020-08-20</signatureDate>
    </ownerSignature>
</ownershipDocument>
