Rooney, 26, scored at both ends but helped United comeback after his own goal in the 11th minute gave the visitors an early advantage. The England international headed one back in the 27th minute as the Red Devils had to comeback from behind once again.
However, Rooney scored his first goal in five appearances in the Premier League. The Manchester United striker is in fine form scoring in three consecutive matches including three for England at the international break against San Marino and Poland.
At the thick of things, Rooney set up goals for Danny Welbeck and Robin van Persie but also scored the fourth as Stoke were closing in after Michael Kightly narrowed United's lead.
Since his record move from Everton to Manchester, Rooney has won the Premier League four times, the Champions League once, the League Cup twice and the Fifa Club World Cup. On his debut for United, Rooney scored a hat-trick in the UEFA Champions league match against Fenerbache.
In 448 club appearances, Rooney has scored 200 goals which include 183 for Manchester United since 2004 while he has also scored 32 goals for England in 78 games.