The new deal will keep Wilson at Old Trafford until the summer of 2019.
The 19-year-old has not played in the league for the United first team since the end of last season, but he remains highly rated at Old Trafford.
Wilson has recently been strongly linked with a loan move away from the club.
United boss Louis van Gaal said at his press conference on Friday: “I think he needs to play but Manchester United’s interests are always higher than individual interests, so I have doubts to let him go.
“And maybe we have to wait until December that we know how it is with our club, (if) we are succeeding in the Champions League, the Capital One Cup, because maybe he shall receive minutes off me because I have to rotate.
“You have seen what I have done against Ipswich Town. It can be done also in the other matches, so I have talked with him and I think that we wait until December.”