The Scotland international, 29, missed most of last season after undergoing surgery for ulcerative colitis, having previously been out for 10 months after being diagnosed with the condition at the end of 2011.
It was worried that the chronic bowel condition would end his career, but Fletcher was back in training last week and trotted out in the Under 21 match at the Salford City Stadium.
Fletcher lasted 67 minutes before being taken off and, despite his return to fitness, he is unlikely to be involved in Tuesday’s Capital One Cup match against Norwich City.
Michael Keane's late equaliser gave United a 2-2 draw against Fulham, who had led 2-0 at one point.
Fletcher had a mixed game, giving the ball away for Moussa Dembele's opener but improving as it went on.
That he lasted over an hour is a major boost though - his last match was the 4-3 win over Newcastle United at Old Trafford last Boxing Day.