Fletcher is battling back to fitness after being sidelined for almost two years by a chronic bowel complaint.
Although the Scot is still believed to be some way short of a return to first-team duty, the outing for United's juniors is a major positive for the club.
David Moyes was on hand to watch the majority of a game that was switched to United's training ground at short notice and in which Fabio and Wilfried Zaha also got some game time.
Meanwhile, United striker Danny Welbeck looks certain to miss England's friendlies against Chile and Germany later this month.
Welbeck has not played since the draw with Southampton at Old Trafford on October 19 due to fluid on his knee.
Moyes has already said the 22-year-old will not feature in Sunday's crunch game with Arsenal at Old Trafford.
Welbeck was selected on Thursday as part of Roy Hodgson's squad for the start of England's World Cup build-up, but it is understood he is unlikely to be involved.