Youngsters Ismael Ehui and Lino Goncalves scored the goals inside the opening 15 mins at Motspur Park.
That was the Cottagers last reserve team game this season.
Fulham line up: Sanna, Moncur, Milsom, Leacock, Watts, Orelaja (Gowland 72), W Brown (Cumber 86), Mabbutt, Miguil (Smith 72), Goncalves, Ehui