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The Portuguese coach was reported to have directed an insult in his native language towards a camera which was live tracking him down the touchline after his side's 3-2 comeback win at Old Trafford.
"It is alleged that his (Mourinho's) language at the end of the fixture, as captured by the broadcast footage, was abusive and/or insulting and/or improper. He has until 6pm on 19 October 2018 to respond to the charge," the FA said in a statement.
Mourinho's punishment, if found guilty, could include a touchline ban, which would mean him sitting in the stands for the game against his former club Chelsea at Stamford Bridge on Saturday.