But the on-loan striker has been ruled out of the trip to Stevenage as Millwall don’t want him cup-tied.
Marquis failed to make the squad for last weekend’s victory over Exeter.
Instead he was seen leaving Fratton before kick off with a bin liner, having said his goodbyes to players and staff.
After talks by the player and Whittingham with parent club Millwall, it has been agreed Marquis will remain for the final two weeks of his loan.
He returned to Blues training yesterday, while in the evening joined the likes of Danny East, Jed Wallace, Dan Butler, Patrick Agyemang and Ricky Holmes watching the Academy’s 12-0 win over Moneyfields.
Marquis is now in the frame for the trip to Newport County in the Johnstone’s Paint Trophy (November 12) and the visit to AFC Wimbledon (November 16).
And Whittingham is adamant he would have no qualms on calling on the striker who has netted twice in six Pompey matches so far.
He said: ‘John never left, what he wanted to do on the Monday was go and talk to Millwall
‘There was a phonecall I put into Millwall. I had a talk to the manager and assistant manager – Mick Harford – and they were going to talk to him.
‘The best result is John is down here for two weeks and getting involved in training.
‘There is no problem at all and I have no issues picking him.
‘He’s not available for the FA Cup but there is a JPT game and there’s one more league game, things happen quickly in football as we all know.
‘Who is to say in a week’s time, when we are playing Newport, we might have illness or injury after the Saturday match, you never know.
‘Still, the situation with John wasn’t clear on Saturday and now we where we stand.
‘John got emotional because he was expecting to be in the squad but wasn’t – for circumstances I have said before.
‘Millwall is his club, he’s their player so we had to make sure they were happy with the situation.
‘He wanted to go and discuss it with them on Monday.
‘That’s what he did and he is back in.
‘They wanted him to keep playing and he is happy to keep doing that.’
Millwall have already stipulated they don’t want him playing against Stevenage.
With Pompey still awaiting clearance for Jake Jervis and Ashley Harris still effectively on loan, it leaves them with four available strikers.
Meanwhile, Whittingham is waiting to learn whether Bury will allow Trevor Carson to play at the Lamex Stadium.
He added: ‘We are finding that out on Trevor at the moment. I’ve not heard yet but haven’t been told no.’