Moussa Dembele proved to be the difference as his hat-trick secured Fulham all three points against the Royals.
Although Uche Ikpeazu hauled Reading back into the game in the second half, 16-year-old Dembele - not to be confused with the Spurs star - scored his third goal in stoppage time to seal the win.
Academy manager Eamonn Dolan was able to welcome back Craig Tanner and top scorer Ikpeazu into the fray - but it was an unfortunate start to the Elite League match for Reading after having a goal disallowed in the third minute for offside.
A defensive mix-up allowed Dembele to slot home with less than 15 minutes played, before the highly-rated Frenchman lashed home a volley to give the Cottagers a two-goal cushion.
Ikpeazu struck the woodwork just before half time during the Royals' dominance either side of the interval. Our youngsters had the ball in the back of the net once again, but had the goal chalked off for a foul in the build up.
Eventually, Reading hit one back. Ikpeazu's well taken penalty, his 18th of the season, gave Reading a deserved glimmer of hope with less than quarter of an hour remaining.
But Dembele tapped home in stoppage time to secure all three points for the hosts. The young Royals will take heart from a valiant fightback ahead of their next Elite League fixture - at home to Bolton this Saturday.
Royals XI: Lincoln; Long, Griffin, Hyam, Cooper; Kuhl, Stacey (Shama 80), Kelly, Fosu; Tanner (Murombedzi 45); Ikpeazu.