Rooney became United's all-time record goalscorer last month as he surpassed Sir Bobby Charlton's total, but the club captain has not started a Premier League match since before Christmas.
The 31-year-old has a contract at Man United until the summer of 2019, but Scholes has claimed that he would not be surprised if his former teammate decided to seek pastures new at the end of the season.
"If it carries on going the way it is, I can't [see him staying for two more years]. Maybe it will be reassessed at the end of the season if he's in and out of the team," Scholes told the Daily Mail.
"I don't see him as a player who will accept that. He will want to be at a team where he's playing every week. No-one will be more frustrated than Wayne at not playing. Being a sub will be driving him up the wall."
Rooney will miss Man United's Europa League last-32 first leg against Saint-Etienne on Thursday night with a 'little muscular problem'.