Boro fielded a team with several experienced Reserves and also included England U-16 stars Nathan Porritt and Jonathan Franks, but they were no match for their Fulham counterparts.
Fulham took an early lead through Bradley Hudson-Odoi and it took almost an hour for Boro to find a deserved equaliser through Josh Walker.
The visitors regained the lead within minutes, through Hudson-Odoi again, and as Boro pushed for a second equaliser Fulham sealed the game, with a third deep into injury time from Andrew Otley.
Boro team:
Pennock, Johnson (McCardle), Grounds, Burgess, Langthorne, Cattermole, Clough, Walker (Fisher), Owens, Porritt, Franks