Mourinho appeared to swear in Portuguese to a television camera as he left the Old Trafford pitch, minutes after Alexis Sanchez's late winner secured an important victory.
The United manager had come under increasing pressure in the hours before Newcastle's visit, with reports claiming he would lose his job in the following days regardless of the result.
An FA statement read: "Jose Mourinho has been charged following Manchester United's game against Newcastle United on 6 October 2018.
"It is alleged that his language at the end of the fixture, as captured by the broadcast footage, was abusive and/or insulting and/or improper."
Mourinho has until 6.00pm on Friday to respond to the charge, which could result in a fine or touchline ban.
United trailed 2-0 against Newcastle with 20 minutes remaining, only to complete a remarkable turnaround through goals from Juan Mata, Anthony Martial and Sanchez.
Mourinho is alleged to have vented his frustrations after the final whistle by mouthing the words ‘fodas filhos de puta’ - 'f*** off, sons of b******' - into the camera while wagging his little finger.
In his post-match interviews, Mourinho claimed to be the subject of a "man-hunt" and complained of "wickedness" within football.
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