After Alex Ferguson announced his shock retirement as United manager on Wednesday, reports emerged that Rooney had informed the Scot of his desire to leave the club in an informal conversation two weeks ago.
However, United dismissed the idea, with a spokesman saying: "Wayne Rooney is not for sale."
The story threatens to derail Rooney's reunion with his former manager at Everton, David Moyes, who was on Thursday expected to be formally appointed as Ferguson's successor at Old Trafford.
Rooney was handed his Everton debut by Moyes in 2002 and joined United two years later in a £27 million ($42 million, 31.9 million euros) transfer that made him the world's most expensive teenage player.
The striker's position at United has fallen under scrutiny in recent weeks after he was left on the bench for a vital Champions League knockout game at home to Real Madrid.
The 27-year-old previously issued a transfer request in 2010, only to change his mind and sign a new five-year contract with United.