Rooney hobbled off in the final few minutes of the game to compound what was a miserable afternoon at Goodison Park.
James McCarthy opened the scoring for Roberto Martinez’s side before John Stones and Kevin Mirallas struck to secure all three points for Everton.
Van Gaal revealed Rooney picked up an injury but insisted United will have to wait to see how “heavy” it is.
When asked if Rooney had an injury, van Gaal said: ”Yes, he was injured. He got a hit on his knee. We have to wait and see how heavy it is.”
Rooney has been in fine form in recent weeks so van Gaal will be hoping he is not out of the starting XI for too long.
Michael Carrick has also been sidelined recently and his absence has negatively affected United’s play. If Rooney is ruled out of action, van Gaal does not have great options when it comes to a replacement. Robin van Persie has only just returned from injury while Radamel Falcao is going through a tough time at Old Trafford.