The Portuguese tactician re-entered the field of play after Ramires was sent off for a challenge on Karim El Ahmadi in the dying stages of the Blues' 1-0 loss at Villas Park.
Mourinho was sent from the touchline by referee Chris Foy and has now been charged by the FA for his actions.
"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.
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