The American striker, who arrived at Fulham in January, scored either side of half-time to end the home team's five-match unbeaten run.
While McBride was clinical, Bolton's Kevin Davies was wasteful, squandering a number of good chances. The victory rounded off a splendid campaign for manager Chris Coleman in his first season in charge.
He took over the reins from Jean Tigana and has made the transition from player to boss with apparent ease. Long-serving midfielder Per Frandsen was named Bolton's captain with his future at the club still uncertain. The 34-year-old Dane is one of a number of players out of contract in the summer.
He was given a standing ovation when he was replaced by Stelios Giannakopolous in the 71st minute - an indication this may have been his last game for the club. Fulham had a scare in the first minute when Jay-Jay Okocha launched a long throw into the area.
The ball was only half-cleared and Nicky Hunt whipped in a shot that went narrowly wide. Fulham hit back and Carlos Bocanegra tried to release Sean Davis but goalkeeper Jussi Jaaskelainen raced out to intercept. Then a delightful move between Hunt and Kevin Nolan ended with Bocanegra making a hasty clearance.
Bolton kept up the pressure and Frandsen was marginally off target with a shot from the edge of the area. Davies, an ever-present in the league, should have put Bolton ahead in the 17th minute after Okocha launched the ball forward. Alain Goma slipped leaving Davies with a clear run on goal but his shot ended in the arms of goalkeeper Edwin van der Sar. A minute later Okocha scuffed his effort wide following a through ball from Frandsen.
The Nigerian playmaker then rattled the bar from a free-kick after Campo was hauled back by Davis. Fulham were being stretched and Davies saw a header from a good position clear the bar. Bolton were playing with the confidence that comes with five successive victories.
Fulham broke quickly in the 39th minute and Moritz Volz weaved his way into the penalty area. Instead of squaring it across the face of the area he went for goal and was crowded out. Bolton responded immediately and Ivan Campo got away from his marker when Youri Djorkaeff swung in a corner, only to head wide.
Fulham took the lead a minute before the break with McBride heading home unmarked at the back post to stun Bolton following a cross from Bocanegra. Ricardo Gardner was given a rousing reception by the home fans when he came on for Simon Charlton at the start of the second half. The Jamaica international only returned to action last week at Everton after a knee operation in January. Gardner quickly settled into the game and got away down the left and tried to pick out Nolan, only for the ball to be scrambled away. Fulham, however, continued to look dangerous on the counter-attack. McBride skipped clear of Emerson Thome but Jaaskelainen was able to make a comfortable save.
Bolton manager Sam Allardyce made another change in the 59th minute bringing on Pedersen for the tiring Djorkaeff. The Danish striker set up Davies three minutes later with a good delivery from the left. Davies, however, could not get any power on the shot and van der Sar made an easy save. Giannakopoulos was foiled by van der Sar two minutes later when the Dutchman pounced on a through-ball from Okocha. Fulham extended their lead in the 78th minute with McBride's second goal of the game. He got on the end of a cross from Davis to steer a shot beyond Jaaskelainen. Davies then steered his effort wide following a good cross from Pedersen in a rousing finish by Bolton. While the defeat was disappointing for the supporters, it should not disguise the fact that the club's progress has been little short of astonishing.