Fletcher, also captain of the Scottish national team, has missed a number of matches this year due to what was believed to be a viral illness but United said his absence was actually down to a chronic bowel condition.
"Over the past year he has had several absence periods which we have attributed to a viral illness in order to respect his right to medical confidentiality. Darren has, in fact, been suffering from ulcerative colitis (a chronic inflammatory bowel condition) for some time preceding this," said a statement on the club's official website.
"He has therefore accepted medical advice to take an extended break from the demands of training and playing in order to afford the best chance possible of achieving full remission once again," the club added.
Fletcher, 27, has been at Manchester United his whole career, developing into one of the club's most combative and disciplined central midfielders.
"We are going to miss two big players in Fletcher and Vidic, I hope they both come back fitter and stronger than ever," United defender Rio Ferdinand said on Twitter.
It was not clear how long Fletcher's break from the game is likely to last.
