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 said: "For obvious reasons I don't accept the charges."
Asked the basis for his defence, the Blues boss added: "I have to do it Monday, I have to do it privately."