The Portuguese was banished from the dugout in the 27th minute of Sunday's 1-1 home Premier League draw with West Ham United after booting a water bottle down the touchline following what he felt was an unjust booking for midfielder Paul Pogba.
"It is alleged his behaviour ... amounts to improper conduct," the FA said in a statement on Monday. "He has until 6pm on 1 December 2016 to respond to the charge."
Mourinho was also dismissed for verbally abusing referee Mark Clattenburg at halftime during a match against Burnley at the end of last month.
The former Chelsea, Real Madrid, Inter Milan and Porto boss was banned from the touchline for one match and fined a total of 58,000 pounds for two separate incidents of misconduct in October.
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He admitted using abusive and/or insulting language towards Clattenburg and was fined 8,000 pounds for the incident and banned from the touchline for one game.
Mourinho was also charged and fined a further 50,000 pounds for comments he made about referee Anthony Taylor ahead of a game against Liverpool.
United are sixth in the Premier League with 20 points from 13 matches, 11 adrift of leaders Chelsea.
Mourinho's team entertain West Ham again in the League Cup quarter-finals on Wednesday.
(Writing by Tony Jimenez, editing by Pritha Sarkar)
