The 18-year-old defender moved to Goodison Park during the transfer window but with the England Under-19 international uncertain of an immediate first-team place, Flitcroft has revealed that there might be a small chance of re-signing Stones on a temporary basis.
Flitcroft told BBC Radio Sheffield: "I'd say there's a chance, not a good chance. Remember, Everton paid good money for him.
"I'd like to think if a few clubs are sniffing around he'd want to come back to some unfinished business here.
"It wasn't part of the deal at the time that he'd come back here. I think David Moyes would like to assess him and see where he's at."
Stones made 22 appearances for Barnsley in the Championship this season before he departed for the Premier League.