United have stressed the move is part of a "planned procedure", but they admit it is "frustrating" for the 28-year-old who has made just two short substitute appearances since starting the Barclays Premier League win at Reading on December 1.
A United statement read: " Darren Fletcher will be unavailable for the remainder of this season having undergone surgery to resolve his ulcerative colitis condition."
The statement continued: "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.
"We would be grateful if his privacy could be respected at this time and in the coming months in order to aid his recuperation."
New Scotland manager Gordon Strachan said Fletcher remains in his thoughts, both on and off the pitch. In a statement, Strachan said: "On behalf of the Scotland supporters, the national squad and backroom team, I wish Darren the best of luck in his recovery from the surgery that has been confirmed by his club.
"I spoke with Darren on Tuesday and know that the decision to have the operation has been taken in the interests of his long-term health and with the full backing of the medical staff at Manchester United.
"Darren's commitment and pride in playing for his country is an example to any professional footballer, as has been demonstrated by his availability for the recent World Cup qualifiers and the international challenge match against Luxembourg.
"I'm sure I speak for all Scotland fans when I say I hope that the operation allows Darren to overcome his condition and resume his role as a major influence for club and country in his own time. In the meantime, I have stressed to him that, as captain, he remains an integral part of the international set-up and that he is welcome to join up with the squad at any time during his recovery."