The 27-year-old has handed in his second transfer request in three seasons and is desperate to leave Old Trafford, but the former club official does not expect the striker to go
Rooney asked to leave United before Sir Alex Ferguson announced his retirement at the start of May and the striker is still determined to leave following the arrival of David Moyes.
Some United fans booed Rooney when he collected his Premier League winner's medal, and also when he boarded the bus for the club's trophy parade around Manchester.
But Sir Alex had insisted before his departure that Rooney would not be sold.
And Gill, who has ended his 16-year professional association with the club in pursuit of other roles, expects the 27-year-old to stay put, despite interest from Chelsea and Arsenal.
"I think as Alex said at his last press conference, that's an issue for David Moyes and the new team to do, but look - I'm confident he'll be there next season," he told Sky Sports.
"I think he's a great great player, it's a great great club and the club doesn't want to lose its star players.
"So I'm sure every bit of work is being taken with Wayne, his advisers and David and Ed [Woodward, Gill's replacement] etc to ensure that happens.
"I'm not a betting man, but I'm confident when I sit in Old Trafford next season I'll be seeing Wayne Rooney running out."