Billy McKinlay's side did just enough to see off a spirited Gunners, who had several regular reserves away with the first team squad, with a late Eddie Johnson penalty sealing the win.
Quickly into their stride Fulham impressed early on with Johnson heading a cleverly chipped pass from Bjorn Helge Riise narrowly wide before the Norwegian international went even closer moments later, lifting Matthew Saunders' through ball over the target.
At the other end the best of the visitor's chances fell to Sanchez Watts who did well to out run Matthew Briggs and meet Chuks Aneke's pass, forcing a corner through his deflected shot.
After a lively start, the game began to settle with Fulham's Andranik controlling the tempo from the middle of the park and doing much to impress the on-watching Roy Hodgson.
While Fulham looked good with a display of clever passing and pressing midfield play, Arsenal caught the eye with their pace and threat on the break with Luke Freeman and Aneke looking particularly threatening.
In fact, it was Freeman who had the Gunners' best chance of the half when he met a teasing cross from the right and forced a fine instinct stop from David Stockdale.
Both sides had chances to take a lead into the break with Michael Uwezu and Eddie Johnson going close, while Emmanuel Frimpong dipped a 25-yard free-kick over the Whites' goal.
After the restart, Johnson blazed high and wide from a narrow angle, while Frimpong's corner from the left curled wide of the back post as both sides looked to showed their attacking intent.
A thumping challenge and weighted pass from Kagisho Dikgacoi then freed Johnson for another chance and the American should have done better with just James Shea to beat on the run.
However, as the half wore on the tempo that promised much in the first period seemingly faded, with three over-hit corners and a goal mouth scramble setting the tone going into the final 15 minutes.
A surging run from Watts drew a clever near post save from Stockdale to breathe life into proceedings, but it was Arsenal that threatened to impose themselves on the outcome keeping possession and exploiting the pace of their front line.
Against the run of play however, Daniel Boateng barged into the back of Andranik from Saunders' quick thinking header and with the referee pointing to the spot, Johnson stepped up and despatched a coolly-taken strike high and into the top left corner.
With 10 minutes left on the clock Arsenal began to look jaded with half chances falling to Uwezu and Riise.
It was by no means pretty, but McKinaly's charges held on for what was just about a deserved three points.
Fulham DS: Stockdale; Marsh-Brown, Anderson, Briggs, Pierre; Dikgacoi, Saunders, Riise, Andranik; Seol (Uwezu 7 Hoesen 83), E.Johnson. (Subs): Bettinelli, Smith, Moscatiello.
Arsenal Reserves: Shea; Hajrovic, Evina, Miguel, Boateng; Frimpong, Deacon (Afobe 87), Henderson, Aneke (Ozyakuo 70); Watt, Freeman. (Subs): Dunn, Yennaris, Meade.
Read more: http://www.fulhamfc.com/Club/News/NewsArticles/2009/December/ReservesvArsenal.aspx#ixzz0lHJZgUPK