Kai Havertz returned to the Arsenal squad after suspension, while Fulham named two former Gunners – Willian and Alex Iwobi – in their starting line-up.
It took the visitors a full five minutes to take the lead when Bukayo Saka finished off a blistering counter-attack to deflect past Bernd Leno.
However, the Cottagers were undeterred and almost got back into the game in the 20th minute when Willian’s effort curled just wide of the post.
And they got their goal on the half-hour when Raúl Jiménez finished off a great team move with a first-time finish from inside the area.
After the break Arsenal looked to have possession again as Fulham almost kept Mikel Arteta’s side at arm’s length whenever he tried to attack.
Fulham, meanwhile, looked dangerous and got their second just before the hour mark when Bobby De Cordova-Reid was first to react in the six-yard box to pounce.
Arsenal Player Rating
David Raya (6/10): Made one great save in the second half. Couldn’t do anything about either goal.
Ben White (4/10): Fulham really targeted the space behind him and got a lot of joy. Tough afternoon for the right-back.
William Saliba (5/10): Not at his best. He looked nervy at times and picked up a yellow card late on for pulling back Wilson.
Gabriel Magalhaes (6/10): Won some big duels and brought the ball out well into midfield. Probably Arsenal’s best defender on the day.
Jakub Kiwior (4/10): Fulham looked to target him. He will be a bit disappointed with Jimenez’s goal. Should probably have done better to get something on the cross. Replaced at half-time.
Declan Rice (5/10): Not at his dominant best and that is probably why there seemed to be more space in front of Arsenal’s back four than usual.
Kai Havertz (4/10): Back in the side after suspension but didn’t make much of an impact. The game passed him by for the large part.
Martin Odegaard (6/10): Some good touches as usual. You felt he was going to be the man to make something happen for Arsenal. Sent one shot just wide.
Bukayo Saka (4/10): Opened the scoring early on, but Robinson played him well. Missed a great chance to make it 2-2 when he put a volley well over which summed up his day.
Eddie Nketiah (3/10): Anonymous in the first half. Didn’t get much service, but didn’t do enough to get into the game.
Gabriel Martinelli (5/10): Great run and shot to set up the goal for Saka. A better display than of late. He looked more threatening when on the ball and it was a surprise to see him go off relatively early in the second half.