Jason Lowe returned to action but it was an otherwise disappointing afternoon for Rovers' Under-21s.
The Rovers midfielder came through a planned 45 minute outing as two goals from Fulham forward Josh Walker gave the visitors all three points at Brockhall.
Rovers thought they had taken the lead inside the first minute when Nathan Delfouneso, one of four seniors on show, crossed into the area, but as Connor Mahoney put the ball in the back of the net from close-range, his celebrations were cut short by the official's flag.
However Damien Johnson's side couldn't build on what had been a bright opening as Fulham took the lead with their first attack of the match.
On eight minutes the visitors gained possession before the ball was threaded through to Walker and he beat Simon Eastwood with a fine finish.
The Rovers keeper denied the Fulham man soon after, saving with his legs after Stephen Humphreys had played him in, before Humphreys himself was narrowly over with a fierce strike.
It wasn't until the latter stages of the first half that Rovers started to threaten once more. Lowe was wide with a shot from distance before an audacious effort from the impressive Lewis Hardcastle just cleared the crossbar with Fulham keeper Marcus Bettinelli struggling to get back.
The last action of the first half saw Connor Thomson go close, but his well struck shot was kept out at the near post.
Willem Tomlinson replaced Lowe at the break, whilst Danny Guthrie and Delfouneso made way on the hour mark with Joe Rankin-Costello and Lewis Mansell coming on.
And it was the home side who showed the greater attacking impetus, but without ever carving out any clearcut openings.
Thomson saw a shot tipped over after cutting in from the left, before a deflected Hardcastle free-kick almost found it's way to the back of the net until Bettinelli showed good reactions.
But less than 60 seconds later it was Fulham who did make their opportunity count as a ball in from the right was deftly glanced on by Walker for his and Fulham's second of the afternoon.
To their credit Rovers continued to look for a way back into the game, but despite getting into some promising positions, they were unable to breach a resolute opposition defence.
"We were pleased with the start as we thought we had scored a good goal but Connor is flagged offside," said U21s lead coach Damien Johnson.
"But then we gave them a chance and to be fair they were clinical and took it.
"That gave them something to hang onto, but whilst we had a go, we just didn't have that little bit of quality at the end to get back into the game.
"We got into good areas, but that final ball needed to be better, we just didn't have that today, and that was probably the difference."
ROVERS: Eastwood, Travis, Askew, Lowe (sub Tomlinson 46 mins), Lavelle (c), Wharton, Mahoney, Guthrie (sub Rankin-Costello 62 mins), Delfouneso (sub Mansell 62 mins), Hardcastle, Thomson.
Subs not used: Platt, Fisher.
FULHAM: Bettinelli, Sheckleford, Pino Soler, Davies, Donnelly, Smile (sub Kwietniewski 20 mins), Adeniran, de la Torre, Walker, Thorsteinsson, Humphrys.
Subs not used: Norman, Redford.
Goals: Walker 8, 80 mins.