Rooney set up the Red Devils' first goal and found the back of the net on his own as his side seized a commanding 3-0 lead at the half in the English Premier League fixture.
Much to the chagrin of the Craven Cottage crowd, United drew first blood in the ninth minute, which portended the match's trend.
A beautifully threaded pass by Red Devils striker Robin Van Persie sneaked past three Cottager defenders, finding Rooney at point-blank range but at an awkward angle to take the shot.
After a few moments' hesitation and some crafty dribbling in front of Fulham goalkeeper Maarten Stekelenburg, Rooney kicked a short cross to a charging Antonio Valencia, who blasted it in for the early advantage.
But Rooney's work was far from done even in the first 45 minutes. The 28-year-old forward wasted little time in running up the score further on the hosts, scoring in the 22nd minute just after Van Persie gave United insurance at the 20th.
Van Persie passed it through a Fulham defender's legs as Stekelenburg held firm at the near post, and all Rooney had to do was tap it in.
All three scores in the flurry of goals were catalyzed by Van Persie, but it was Rooney who made the defining play on the first one and finished the job on the third.
Since possession was roughly even in the first half of the match, it is even more impressive that Rooney and Co. were able to capitalize on their chances so well. That is evidence of an efficient Red Devils attack firing on all cylinders, spurred by a star in Rooney sporting supreme form.
Although conservatism crept in when United protected the lead in the second half, it is worth bearing in mind that this club is still in transition under new manager David Moyes.
Getting the three points away from Old Trafford is as much as the Red Devils could have desired, and Rooney was a huge reason why the result went in United's favor.