Goals from Keanu Marsh Brown, Michael Uwezu and Chris Buchtmann were enough to hand Billy McKinlay's side all three points.
The Whites started the game in fine fashion and took the lead in the fourth minute through Marsh Brown, who rounded off a good Fulham move with a crisp finish.
Fulham doubled their advantage after 30 minutes when a nice attacking move down the right flank allowed Marsh Brown to feed the ball into the path of Uwezu who finished well from close range.
As the game approached half-time, the home side managed to pull a goal back when Louis Moult reacted quickest in the box and fired past Neal Etheridge.
Fulham continued their search for a third goal following the half-time interval and they deservedly re-established a two-goal cushion on 57 minutes when Chris Buchtmann's free-kick was diverted past Stoke goalkeeper Dave Parton.
The goal was enough to guarantee all three points for the Whites, indeed they could have added to their tally but for the goalkeeping heroics of Parton.
David Elm also showed no ill effects following his recent virus and produced a hard-working performance up front. The Swedish striker led the line well along with Michael Uzewu.
Speaking after the match, Fulham's Reserve Team manager Billy McKinlay gave his reaction to the victory:
"We were deserved winners on the night after a really good performance," he said. "It was a difficult night to play football due to the pitch but we wanted to get out of the traps early. We played some really good football in the early part of the game and getting the goal settled us in.
"The fact that we were playing some good football and causing them problems on a very difficult surface pleased me. Stoke were putting us under a lot of pressure, they were working really hard.
"The goal before half-time got them back into the game and gave them a lift. It was slightly disappointing from our point of view to concede a set-piece. But, once again, we worked really hard to earn the right to play and after Chris' goal we created numerous chances and probably should have won by a greater margin."
Fulham Reserves: Etheridge, Marquez-Sanchez, Briggs, Pierre, Toure, Pritchard, Marsh Brown, Buchtmann, Uwezu (Trotta 75), Elm (Payne 87), Smith (Harris 84). Subs (Unused): Bettinelli.
Read more: http://www.fulhamfc.com/Club/News/NewsArticles/2010/April/StokeResvFulhamRes.aspx#ixzz0laOQlFFd