The 27-year-old striker has been linked with a move away from Old Trafford after retiring manager Sir Alex Ferguson - who will be replaced by Everton boss David Moyes in July - claimed the player had submitted a second transfer request in nearly three years.
The club later revealed the request had been turned down with talks over a new contract well under way, with new UEFA member Gill insisting "every bit of work" is being done to prolong the England international's nine-year stint in Manchester.
Speaking to Sky Sports News at UEFA's Congress in London, Gill said: "As Alex said at his last press conference, that's an issue for David Moyes and the new team but I'm confident he'll be there next season.
"I think he's a great, great player at a great, great club and the club doesn't want to lose its star player.
"I'm sure every bit of work is being taken with Wayne and his advisors to ensure that happens. I'm not a betting man but I'm confident I'll sit at Old Trafford next season and see Wayne Rooney running out."
Liverpool-born Rooney agreed a five-year contract running to June 2015 after changing his mind over leaving the club in October 2010.