After a hugely successful campaign for Terry McPhillips' under 18s, they put in one of their most disappointing displays of the season as they lost the Craven Cottage clash 2-0.
The first half was high on effort but low on quality, but what quality that was on display came from the home side, the closest they came to breaking the deadlock was right on half-time when Sean Kavanagh's free-kick deflected off the wall and then off the woodwork.
The second half saw Rovers raise their game but it was Fulham who broke the deadlock by taking advantage of some sloppy play by Hugo Fernandez. The Spaniard attempting a back heel on the edge of the his own area only for the ball to be robbed and passed to Cauley Woodrow who made no mistake as he swept the ball into the far corner.
Rovers had the opportunity to hit back immediately when a ball over the top saw Raheem Hanley get the better of Josh Pritchard, but with just the goalkeeper to beat the midfielder poked wide of goal.
McPhillips' side pressed for an equaliser, Curtis Haley headed onto the roof of the net whilst Hugo Fernandez stung the gloves of goalkeeper Roberts, but it was the home side that grabbed the all-important second goal seven minutes from time.
Boumesca Tue Na Banga advanced down the right and as he centred the ball was missed by substitute Corey Gameiro but the impressive Ryan Williams didn't and the midfielder fired home despite the best of efforts from Peter Wylie.
It was almost 3-0 two minutes later when Gameiro saw his shot cleared off the line, but any hopes of an unlikely comeback ended when John O'Sullivan was sent off after two bookings.
In the end the hectic schedule of the last few weeks had taken it's toll on the young Rovers, but nevertheless it has still been a successful campaign for the Academy, it is just a pity it couldn't be reflected with silverware as for the second time in a week they watched on as the opposition lifted the trophy.
FULHAM: Roberts, Brister, Kavanagh, Christensen (sub Sambou 87 mins), Grimmer, Pritchard, Williams (sub Banya 89 mins), Minkwitz (c), Woodrow (sub Gameiro 82 mins), Altman, Tue Na Banga.
Subs not used: Tankovic, O'Reilly.
ROVERS: Dilo, Wylie, Beesley, Hanley, Edwards (c), O'Connell, Cotton (sub Cham 69 mins, Lenihan (sub Boland 46 mins), Haley, O'Sullivan, Fernandez (sub Payne 82 mins).
Subs not used: Urwin, Mason.
Booked: O'Connell, Beesley, O'Sullivan, Hanley, Edwards (Rovers).
Off: O'Sullivan (Rovers).