The 31-year-old has been ruled out of United's Europa League quarter-final clash with Anderlecht on Thursday after failing to recover from the ankle issue, which has sidelined the midfielder for the past two games.
With Premier League leaders Chelsea visiting Old Trafford on Sunday afternoon, Mourinho has admitted he isn't yet sure whether Rooney - who did not travel to Belgium - will be able to make his matchday squad for the game.
"He’s not happy with his condition, he’s trying to work with the team, which he does, but he's not confident, not happy," Mourinho said on Wednesday.
"He has a bad feeling with his ankle and is not ready to play. Let’s see for the weekend or the next game. We don’t have many players fit but for tomorrow? No."
David De Gea, who missed United's 3-0 win at Sunderland at the weekend due to a "small" hip problem, has travelled with the United squad for the club's game with Anderlecht although Phil Jones (toe), Chris Smalling (knee), Juan Mata (groin) and Ashley Young (knock) are all sidelined.
Antonio Valencia, however, should feature in the Europa League after returning from a two-game absence due to injury and training normally on Wednesday morning.