It is alleged Mourinho's behaviour in re-entering the field of play in or around the 90th minute of the fixture at Villa Park and approaching referee Chris Foy amounted to improper conduct.
"Jose Mourinho has been charged by The FA following his side's game against Aston Villa on Saturday 15 March 2014," the FA said in a statement on Wednesday.
"It is alleged the Chelsea manager's behaviour in re-entering the field of play in or around the 90th minute of the fixture and approaching the match referee amounted to improper conduct."
Mourinho has until 6pm on 24 March 2014 to respond to the charge.
Managers must not leave their technical area during the match, according to FA rules, but Mourinho pointed out that several people had gone on to the pitch.
"I was two-three metres inside the pitch or four-five metres, but there was like 10 persons there. It was me, my two assistants, (Villa boss) Paul Lambert, Paul's assistants," he said.
"And there was [Gabriel] Agbonlahor, who come in and made an aggression on Ramires from behind.
"So if I was sent off because I was on the pitch, I ask why not the others, especially one player that made an aggression on another one, Agbonlahor on Ramires?"
Mourinho also confirmed he tried to speak to Foy after the game.
He said on Monday: "I tried to speak to Mr Foy twice. I tried to speak on the pitch and I tried in the dressing rooms.
"In the dressing rooms I tried to ask politely, can you give me five seconds? And he refused."