The Football Association announced the charge, which comes after Moyes said United were "playing referees as well as the opposition" following his side's third defeat in a row.
An FA statement read: "Manchester United manager David Moyes has been charged for misconduct by The FA in relation to post-match media comments he made following his side's game against Sunderland on Tuesday 7 January 2014.
"It is alleged the comments called into question the integrity of the match officials appointed to that fixture and/or appointed to Manchester United fixtures generally, and/or implied that such match officials are motivated by bias; and/or brought the game into disrepute, in contravention of Rule E3(1)."
Moyes has until 6pm on January 15 to respond to the charge.
Moyes issued his blast after questioning the awarding of a free-kick that led to Sunderland's opening goal and a penalty. It followed the United manager saying it was "scandalous" his side were not awarded a late penalty against Tottenham at Old Trafford.
He said on Tuesday: "I feel we are having to play the opposition and the referees. We are all just laughing at them at the minute."
Liverpool boss Brendan Rodgers was fined £8,000 and warned as to his conduct on Thursday after admitting a similar charge.