Ancelotti confronted referee Chris Kavanagh on the pitch at full time after Everton were denied what would have been a late winner by Dominic Calvert-Lewin.
Gylfi Sigurdsson was adjudged to be obstructing the view of United goalkeeper David de Gea while in an offside position and following a VAR review the goal was chalked off.
An FA statement read: "Carlo Ancelotti has been charged with misconduct for a breach of FA Rule E3.
"It is alleged that the Everton FC manager's language and/or behaviour on the field of play at the end of the Premier League fixture against Manchester United FC on Sunday 1 March 2020 amounts to improper conduct.
"He has until Thursday 5 March 2020 to provide a response."
Ancelotti said after the game: “Honestly, it was a difficult decision. I think they check the position of Gylfi – that was offside. But in our opinion it didn’t affect the vision of the goalkeeper. In their opinion it affected the vision and the movement of the goalkeeper.”
Ancelotti becomes the first Premier League manager to be shown a red card after the rule was introduced at the beginning of the season.
The 60-year-old will however avoid a touchline ban and will be in the dugout when Everton visit his former club Chelsea this weekend but will be fined £8,000 if he accepts the charge.
