Second half goals by Jesse Lingard and Paul Pogba gave United's youngsters a chance of completing the job in the return leg of the FA Youth Cup semi-finals at Old Trafford.
Chelsea led 2-0 at the break through goals by defender Nathaniel Chalobah and, after Lingard pulled one back, Bobby Devyne put the holders firmly in the driving seat. However, Pogba's header gives Paul McGuinness' side real hope ahead of the second leg on Wednesday week.
Sam Johnstone was quickly called upon to beat out a Milan Lalkovic diving header but the Reds responded with Will Keane lobbing over and Lingard forcing Jamal Blackman into a diving save.
Johnstone and Sean McGinty somehow managed to thwart Lalkovic during a goalmouth scramble and the slippery Slovakian again tested the keeper after a long-range Tom Kane effort also worked the United No1. The breakthrough arrived from the corner after Johnstone had kicked away Lalkovic's shot as the keeper juggled with Josh McEachran's flag-kick to allow Chalobah to gratefully net from close range.
Will Keane could only wastefully prod at a golden opportunity on 38 minutes after a lapse by Chalobah and, four minutes later, the Blues centre-back really made him pay by looping a header over Larnell Cole on the line from George Saville's corner.
Ryan Tunnicliffe forced a diving stop out of Blackman but United knew they had to improve after the break and they did just that. Blackman tipped away a Gyliano van Velzen drive and Pogba dallied after a barnstorming run by Tunnicliffe to lose the chance to score.
Some typically eye-catching skill by Pogba allowed the Frenchman to again sting Blackman's fingertips and it was no surprise when Cole's corner fell to Lingard at the far post and he calmly converted a well-judged half-volley.
United's tails were up but Will Keane dragged wide after a promising break and Blackman got behind another attempt by Pogba. Instead, Chelsea scored against the run of play when Aziz Deen-Conteh burst down the left to tee up a simple finish for the unmarked Devyne for 3-1.