The tie was goalless at half-time but sprang to life in the 40th minute when Floyd Samba curled a superb free-kick up and over the United wall and into the top corner. The response was almost immediate — Godwill Kukonki headed in from close range from a Jim Thwaites cross to level within minutes.
The second half was tight and competitive, with Manchester City growing into it as the hour mark passed. Manchester United's goalkeeper Cameron Byrne-Hughes made a crucial save from Teddie Lamb early in the first half and the woodwork denied City later on. With extra time approaching, Heskey cut inside and drove the ball into the top corner on 87 minutes to seal it.
Head coach Oliver Reiss was emotional afterwards.
"I'm feeling top, happy and proud. It's unbelievable really. The way we won such a special final — I am very proud."
"It was two top teams facing each other and maybe there were a few nerves in the first half which is understandable. I think we were able to increase our intensity and energy in the second half — as we have done a lot this season — and that was key."
"To win at home at the Joie Stadium in front of our supporters was special."
It is City's fifth FA Youth Cup win in total, following triumphs in 1986, 2008, 2020 and 2024. The final came almost exactly 40 years after the clubs' only previous meeting in the competition — also won by City. Both Pep Guardiola and Michael Carrick were in the stands, along with a number of first-team players from both sides.
United's JJ Gabriel, the U18 Premier League Player of the Season and the standout individual talent of the competition, could not find a way through on the night despite linking well at times with Chido Obi.
City's academy director Thomas Kruecken was full of praise for Reiss and his players.
"Winning the FA Youth Cup is always a key target for us at the start of each season. Our results throughout the competition have shown how much it means to Oliver, his staff and the players. It has been a pleasure to watch the team grow and play football that mirrors our ethos here."
Guardiola added his own congratulations to the group.
The triumph adds to City's Under-18 Premier League North title, claimed earlier this month. Reiss's side now prepare for the Under-18 national final against Chelsea next Friday, with the possibility of a league and cup double still within reach.