The in-form striker initially injured his ankle in United's 2-1 defeat by Bayern Munich in the first leg of the Champions League quarter final on March 30.
He was expected to be sidelined for between three and four weeks but he surprisingly played in the second leg just a week later.
He was injured again and had to be substituted ten minutes after the restart as Bayern advanced to the semis on the away goals rule after losing 3-2 at Old Trafford.
"I don't think it's as serious as we said the first time, but I think he’ll be ready for the (Manchester) City game," United coach Alex Ferguson told the pre-match news conference.
"We've got more time to work on it, anyway. Other than that everyone else is fit."
England striker Rooney has been in an inspirational form this season, scoring 34 goals in all competitions.
United are two points behind Premier League leaders Chelsea with five matches remaining.