Mourinho was sent to the stands by referee Anthony Taylor during Chelsea's 4-1 Premier League victory over Cardiff at the weekend, having complained about time-wasting from the Welsh club.
An FA statement read: "Chelsea manager Jose Mourinho has been charged with improper conduct in relation to his behaviour during his side’s game against Cardiff City on Saturday 19 October 2013.
"Mourinho has until 24 October at 6pm to respond to the charge."
After declining to face the media following the Cardiff fixture, Mourinho elaborated on his frustration in a press conference on Monday ahead of Chelsea's UEFA Champions League meeting with Schalke.
"If I was in that (Cardiff) game and if I was paying for my ticket, I would be worried by the fact every time the ball was out or stopped and our opponent had to put the ball in, it took (an average) of 21.5 seconds," said the Portuguese.
"That's a waste of money. You pay your ticket and every time the game stops you have to wait about half a minute.
"When you multiply that for the number of times the game was stopped, you pay for 90 minutes but you get 55 or 60. For me, that breaks the rules."
