Chris Coleman came to Highbury and clearly ordered his side to take on the North Londoners, who do not yet seem to have got into their stride.
His adventurous plans appeared to suffer a setback when Zat Knight was judged to have hauled down Thierry Henry seven minutes into the game. The relief on the Fulham manager's face was evident when Arsenal right-back Lauren hit a tame penalty, comfortably saved by keeper Tony Warner.
The penalty save seemed to spur the visitors, who were not slow to attack the Gunners at every opportunity. Arsenal's clearest chance in the opening exchanges was a 25-yard first-time drive from youngster Cesc Fabregas, but the stinging effort was well parried by Warner.
The Cottagers' positive play was rewarded on 21 minutes when Claus Jensen was gifted possession on the left side of the penalty area, and just as he did with Charlton five years ago, curled a shot into the top-right corner of the net giving Jens Lehmann no chance for the opening goal.
Further encouraged after taking the lead Fulham continued to press ahead, and Moritz Volz's thunderbolt just before the half hour saw Lehmann pull off an instinctive save to deny his fellow countryman.
The Gunners found unlikely relief through Pascal Cygan, who was a surprise replacement for Philippe Senderos. The Frenchman accelerated past Henry to meet a Dennis Bergkamp free-kick that was floated in from the left flank to power his header beyond a helpless Warner.
Fulham, however, were not deterred, and striker Brian McBride, who was put in on goal by former Gunner Luis Boa Morte, fired just wide when he really should have scored.
Similarly, Steed Malbranque, who also found himself in a good position, squandered the opportunity and saw his shot roll wide of Lehmann's goal.
The first half finished on a moment of controversy when Bergkamp was booked for apparently knocking the flag out of the linesman's hands. TV pictures did not show the Dutchman acting deliberately, but referee Mark Clattenberg did not hesitate to show the yellow on hearing his assistant's complaints.
The Gunners began the second half brightly and were rewarded with a goal eight minutes after the restart after Fabregas lofted a delightful ball forward into the path of Henry, who in an instant shot the ball low across the oncoming Warner for the ball to finish in the bottom left corner of the net.
Once again however, Fulham were not deterred and Lehmann was forced to make a point-blank save from a McBride header that looked goalbound the moment it cannoned off the American's head.
The Gunners, clearly relieved, redoubled their efforts and took more control of the game. Gilberto, Bergkamp and Henry all tested the Fulham keeper in quick succession and another goal looked imminent.
The Arsenal fans were not disappointed when Henry struck on 82 minutes to bring himself within one goal of Ian Wright's goalscoring record.
Substitute Mathieu Flamini robbed Boa Morte of possession before threading a ball between the flatfooted Fulham defence for Henry to lift over the oncoming Warner for 3-1.
The victory was sealed by Cygan, who doubled his Arsenal career goals tally when he netted his second of the game in injury time with a close-range volley.