Mikel Arteta’s side crashed out 5-3 on penalties in an incredible fourth round upset after the tie finished 1-1 in normal time.
Arsenal’s Bruno Guimaraes had his penalty saved by Jay Lynch in the shoot-out and Conor Haughey scored Fleetwood’s winner.
Aaron Loupalo-Bi’s first-half goal had put Fleetwood ahead before Viktor Gyokeres equalised after the interval.
Arsenal’s 16-year-old rising star Max Dowman was sent off for violent conduct in the closing stages.
Arteta paid the price for prioritising Sunday’s Premier League trip to Liverpool as his decision to make nine changes backfired spectacularly.
No one would have predicted Arsenal’s embarrassment regardless of Arteta’s selection gamble.
They had moved level on points with Premier League leaders Manchester City after a 2-0 victory over Everton on Saturday.
But instead of extending their run of 11 wins from their 13 previous games, Arsenal returned to north London red-faced after a loss that ranks among the darkest days in the club’s glittering history.
Fleetwood boss Matt Lawlor wept tears of joy as disbelieving fans flooded the pitch to celebrate their club’s astonishing victory.
Only Myles Lewis-Skelly and Viktor Gyokeres kept their places from the Everton game, with teenagers Dowman and Marli Salmon starting, while 18-year-old winger Ceadach O’Neill made his debut.
Languishing in 18th place in League Two, Fleetwood had lost their previous two league games against Exeter and Cheltenham, yet they showed no signs of being intimidated by their illustrious visitors.
After an eight-minute delay due to an unauthorised drone flying over the stadium, Arsenal were caught cold on a windy night by the Irish Sea.
Fleetwood are nicknamed the ‘Cod Army’ in reference to the town’s fishing industry, so it was somewhat fitting that a mistake from Salmon netted their opener in the 21st minute.
Salmon’s lack of experience was brutally exposed when Loupalo-Bi muscled his way past the 17-year-old with ease, racing into the penalty area to plant a low finish past debutant keeper Illan Meslier.
Arsenal monopolised possession after that shock, but Arteta grew visibly agitated with their lack of cutting edge.
Arteta sent on Martin Odegaard at half-time and Gyokeres bagged Arsenal’s equaliser five minutes later.
It was a scrappy effort that left Fleetwood feeling aggrieved as Gyokeres wrestled with his marker before poking O’Neill’s ball past Lynch from close-range.
Dowman saw red in the 85th minute, dismissing for kicking out at Harrison Neal after a strong challenge from the Fleetwood midfielder.
Although it looked a harsh decision, Arteta was unimpressed with Dowman, giving him a stern word as the midfielder trudged off.
Both teams scored their first three penalties in the shoot-out, but Guimaraes was denied by Lynch and Haughey held his nerve to seal the biggest shock in League Cup history. (AFP)
