The Chelsea boss was sent to the stands in the victory over Cardiff City after verbally abusing referee Anthony Taylor over a time-wasting issue and may face a touchline ban.
Mourinho was sent to the stands after berating referee Anthony Taylor for warning Branislav Ivanovic over time-wasting. Mourinho was forced to watch the remaining 20 minutes from the East Stand among Chelsea fans but may now face a touchline ban following the FA's statement.
It read: "Chelsea manager Jose Mourinho has been charged with improper conduct in relation to his behavior during his side's game against Cardiff City on Saturday 19 October 2013. Mourinho has until 24 October at 6 p.m. (local time) to respond to the charge."
Assistant manager Steve Holland fielded questions in the postmatch press conference and attempted to explain Mourinho's actions.
"Jose is very frustrated and it stems from the time-wasting from the opposition from basically the first two or three minutes of the game," Holland told reporters. "We mentioned it to the fourth official in a professional way on countless occasions.
"The referee didn't appear to do anything about it but when we had a throw-in, Ivanovic had the ball in his hands for two seconds, and the referee was about getting the ball back into play and pointing at his watch.
"So it was a case of huge frustration with that. And to be sent off for that was very harsh."