If you want to generate JWT from x509 cert/key, any operation (including reading) on %SYS.X509Credentials requires U on %Admin_Secure resource.%Admin_Secure is required because %SYS.X509Credentials is persistent, and it's implemented this way to prevent all users from accessing private keys.

If %Admin_Secure resource is not available at runtime, you can use the following workaround.

Upon reviewing the code for JWT generation, I discovered that the JWT code utilizes %SYS.X509Credentials solely as a source of runtime data for PrivateKey, PrivateKeyPassword, and Certificate. As a workaround, you can use a runtime non-persistent implementation of the X.509 interface, exposing just these properties. If you're using interoperability Cert/PK can be stored in credentials for secure access:

Class User.X509 Extends %RegisteredObject
{

Property PrivateKey As %VarString;

Property PrivateKeyPassword As %String;

Property Certificate As %VarString;

Property HasPrivateKey As %Boolean [ InitialExpression = {$$$YES} ];

ClassMethod GetX509() As User.X509
{
    set x509 = ..%New()
    set x509.PrivateKey = ..Key()
    set x509.Certificate = ..Cert()
    quit x509
}

/// Get X509 object from credential.
/// Username is a Cert, Password is a Private Key
ClassMethod GetX509FromCredential(credential) As User.X509
{
    set credentialObj = ##class(Ens.Config.Credentials).%OpenId(credential,,.sc)
    throw:$$$ISERR(sc) ##class(%Exception.StatusException).ThrowIfInterrupt(sc)
    
    set x509 = ..%New()
    set x509.PrivateKey = credentialObj.Password
    set x509.Certificate = credentialObj.Username
    quit x509
}

ClassMethod Key()
{
    q "-----BEGIN RSA PRIVATE KEY-----"_$C(13,10)
    _"YOUR_TEST_KEY"_$C(13,10)
    _"-----END RSA PRIVATE KEY-----"
}

ClassMethod Cert() As %VarString
{
    q "-----BEGIN CERTIFICATE-----"_$C(13,10)
    _"YOUR_TEST_CERT"_$C(13,10)
    _"-----END CERTIFICATE-----"
}

}

And you can generate JWT the following way:

ClassMethod JWT() As %Status
{
    Set sc = $$$OK

    //Set x509 = ##class(%SYS.X509Credentials).GetByAlias("TempKeyPair")
    Set x509 = ##class(User.X509).GetX509()
    
    Set algorithm ="RS256"
    
    Set header = {"alg": (algorithm), "typ": "JWT"}
    Set claims= {"Key": "Value" }
    
    #; create JWK
    Set sc = ##class(%Net.JSON.JWK).CreateX509(algorithm,x509,.privateJWK)
    
    If $$$ISERR(sc) {
        Write $SYSTEM.OBJ.DisplayError(sc)
    }

    #; Create JWKS
    Set sc = ##class(%Net.JSON.JWKS).PutJWK(privateJWK,.privateJWKS)
    
    If $$$ISERR(sc) {
        Write $SYSTEM.OBJ.DisplayError(sc)
    }

    Set sc = ##Class(%Net.JSON.JWT).Create(header,,claims,privateJWKS,,.pJWT)
    
    If $$$ISERR(sc) {
        Write $SYSTEM.OBJ.DisplayError(sc)
    }
    
    Write pJWT
	Return sc
}

Alternatively you can use dynamic object to skip class creation, in that case it would look like this:

ClassMethod JWT(credential) As %Status
{
    Set sc = $$$OK

    //Set x509 = ##class(%SYS.X509Credentials).GetByAlias("TempKeyPair")
    Set credentialObj = ##class(Ens.Config.Credentials).%OpenId(credential,,.sc)
    throw:$$$ISERR(sc) ##class(%Exception.StatusException).ThrowIfInterrupt(sc)
    
    Set x509 = {
        "HasPrivateKey": true,
        "PrivateKey": (credentialObj.Password),
        "PrivateKeyPassword":"",
        "Certificate":(credentialObj.Username)
    }

    Set algorithm ="RS256"
    
    Set header = {"alg": (algorithm), "typ": "JWT"}
    Set claims= {"Key": "Value" }
    
    #; create JWK
    Set sc = ##class(%Net.JSON.JWK).CreateX509(algorithm,x509,.privateJWK)
    
    If $$$ISERR(sc) {
        Write $SYSTEM.OBJ.DisplayError(sc)
    }

    #; Create JWKS
    Set sc = ##class(%Net.JSON.JWKS).PutJWK(privateJWK,.privateJWKS)
    
    If $$$ISERR(sc) {
        Write $SYSTEM.OBJ.DisplayError(sc)
    }

    Set sc = ##Class(%Net.JSON.JWT).Create(header,,claims,privateJWKS,,.pJWT)
    
    If $$$ISERR(sc) {
        Write $SYSTEM.OBJ.DisplayError(sc)
    }
    
    Write pJWT
    Return sc
}