The Blues had trailed 3-2 after the first leg at Craven Cottage, but thanks to goals from Charlie Colkett, Jordan Houghton, Isak Ssewankambo and a Dominic Solanke brace, they were able to turn the tide around to win 5-3 on the night, 7-6 on aggregate, to be crowned champions.
Chelsea may have finished the game holding the trophy, but it could very well have been Fulham's after the Cottagers took an early lead at Stamford Bridge.
Moussa Dembele opened the scores after just five minutes, making it 4-2 on aggregate. Colkett's penalty and a long-range effort from Houghton put Chelsea ahead on the night, but Fulham soon rallied to take a 3-2 lead into the break with goals from Patrick Roberts and Solomon Sambou.
It seemed it would remain that way as, despite all their efforts, Adi Viveash's side couldn't find a break through and Fulham themselves impressed on the break, causing problems.
With 13 minutes remaining, however, Ssewankambo's piledriver gave Chelsea hope.
At 3-3, the Blues still needed one more goal to draw level on aggregate, and it came through a Solanke header on 82 minutes.
The 16-year-old was on the score sheet again, too, smashing home beyond Fulham goalkeeper Marek Rodak two minutes into time added on, securing a memorable victory.
There were plenty of highlights over the two legs of this year's FA Cup Youth Cup final. Bleacher Report looks at five Chelsea players who impressed.