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.
United said Fletcher had managed to keep his symptoms under control for long periods but that this had proved more difficult recently.
"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.
His absence will be a further blow for United manager Sir Alex Ferguson who is currently without injured midfielders Anderson and Tom Cleverley, strikers Javier Hernandez and Michael Owen, and Brazilian defenders Rafael and Fabio da Silva.
Captain and central defender Nemanja Vidic has been ruled out for the rest of the season with a knee injury.
"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.
United are two points behind Manchester City at the top of the Premier League and have qualified for the Europa League after failing to reach the Champions League knockout stages.
