Fletcher ruled out for rest of season
The 28-year-old Scotland international missed most of last season and the start of the current campaign because of the problem but returned to make 13 appearances for club and country since September.
His last match was an 89th-minute substitute appearance in United's 4-3 win over Newcastle on December 26.
"Darren Fletcher will be unavailable for the remainder of this season having undergone surgery to resolve his ulcerative colitis condition," the club said in a statement on their website.
"We wish to stress this was a planned procedure undertaken at the optimal time having achieved a period of sustained good general health, as illustrated by the fact that Darren has trained with the team regularly this season and been available for selection right up to the operation.
"Whilst it is frustrating for both Darren and the club that he won't be able to contribute further during this campaign, this decision has been taken with our full support in the best interests of his long-term health and we look forward to him returning next season with this problem firmly behind him," the statement added.