The Red Devils have until Monday to respond to the charges.
Manchester United have been charged with improper conduct by their players during the FA Cup win over Fulham.
The charge relates to the moment when Willian’s handball denied Jadon Sancho a clear chance to equalize. Several United players surrounded referee Chris Kavanagh as they protested against Willian’s action.
"Manchester United have been charged after their players surrounded a match official during the 71st minute of the FA Cup tie against Fulham on Sunday, March 19," an FA statement read.
"It's alleged that Manchester United failed to ensure its players conducted themselves in an orderly fashion and/or do not behave in a way which is improper. Manchester United has until Monday, March 27 to respond."
The drama saw Fulham manager Marco Silva and Aleksandar Mitrovic – who had given Fulham the opener - sent off. The Red Devils went on to win the match 3-1 and progress to the semi-finals.
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The striker is facing a lengthy ban after he gave the referee a push and was consequently charged with violent and improper conduct.
On Monday, a statement released read: "Fulham, Marco Silva, and Aleksandar Mitrovic have been charged following the incidents that took place in or around the 72nd minute of their tie against Manchester United in the FA Cup on Sunday, March 19.
"It’s alleged that Marco Silva used abusive and/or insulting words and/or gestures and/or behaviour towards the match referee; that he used abusive and/or insulting words towards the fourth official prior to his dismissal; and that he also used abusive and/or insulting words and/or gestures and/or behaviour towards the fourth official after being sent off.
"It’s further alleged that in throwing a water bottle in the direction of the assistant referee his behaviour was improper."