Mourinho had made inappropriate comments on the referee prior to Manchester United match against Liverpool in the game week 8.
Prior to the match against arch-rivals, Jose Mourinho had said: "I think Mr Taylor is a very good referee but because such pressure is being put on him I think it will be difficult for him to have a very good performance at Anfield," he said.
"I don't really want to say too much more on the matter. I have my view but I have learned a lesson, if you want to call it that, by being punished so many times for my words about referees."
FA released an official statement which read: "Manchester United manager Jose Mourinho has been charged with misconduct, in respect of comments he made relating to the appointed match referee prior to the Liverpool FC v Manchester United FC fixture on Monday 17 October 2016.
"It is alleged his comments were improper and/or brought the game into disrepute contrary to FA Rule E3(1). Mr. Mourinho has until 6pm on Monday 31 October 2016 to respond to the charge."
The FA's official tweet read
This is not the first time that Mourinho has been charged for his inappropriate comments on the match officials. He has been booked on several occasions previously for similar behaviour.