Van Gaal said after the game that "every aspect of the match" had been "against" his team, including the referee Chris Foy.
A statement from the FA on Wednesday said it was alleged that Van Gaal's words "allege and/or imply bias on the part of the match referee and/or bring the game into disrepute".
The Dutchman has until 6pm on Monday to respond to the charge.
Source : PA
Source: PA