The 52-year-old Portuguese has until Thursday at 6pm to respond to the charge, which relates to his half-time dismissal by referee Jonathan Moss at West Ham last Saturday.
Mourinho is already appealing against a Â£50,000 fine and suspended one-match stadium ban for comments made about referee Robert Madley following the Southampton defeat.
The Blues may comment following Tuesday night's Capital One Cup fourth-round tie at Stoke, where he will be looking for a response from the loss to revive his bleak-looking prospects in his job.
Four games prior to November's international break - two trips to Stoke take place either side of home matches against Liverpool and Dynamo Kiev - could determine whether Mourinho has a future with the London club or not.
Saturday's Barclays Premier League clash with Jurgen Klopp's Reds could be key, so too the Champions League clash with Dynamo Kiev on November 4.
Mourinho signed a new four-year contract on the eve of the season-opener with Swansea, but 59 days later, after a 3-1 loss at home to Southampton on October 3, he was subject of the first vote of confidence in a manager in Roman Abramovich's 12-year ownership.
The club's October 5 statement expressed support in the Portuguese, but stressed results had to improve and he had the squad to do it.
Chelsea have won one of their three games since, against a free-falling Aston Villa, and are 15th in the Premier League after losing half of their 10 games.
Mourinho has found solace in the League Cup before
It is a competition he has won three times, most recently against Tottenham in March.
Nemanja Matic missed the Wembley final through suspension and is again banned after his red card at Upton Park.
Mourinho is unlikely to revert to the largely second-string side chosen at Walsall, with Ruben Loftus-Cheek or John Obi Mikel likely to come in for Matic.
Mikel performed well at West Ham when he came on at half-time for Cesc Fabregas.
Chelsea, who must pay a fine of Â£25,000, imposed automatically for six or more bookings, had been reduced to 10 men by then after a first-half implosion which has prompted the charges from the FA.
Mourinho has been charged "in relation to his language and/or behaviour towards the match officials in or around the dressing room area at half-time" at Upton Park
If found guilty, it would not trigger the stadium ban, which relates specifically to media comments.
Silvino Louro, one of Mourinho's assistants, was sent to the stands after Matic's dismissal and has also been charged with misconduct.
Both the Hammers and the Blues have also been charged for failing to control their players in the aftermath of the challenge which led to Matic's dismissal.
All parties have until Thursday at 6pm to respond to the charges, which are likely to ensure Mourinho's relationship with the FA deteriorates further.
Mourinho perceives inconsistencies in the FA's disciplinary process and called for his relationship with the governing body to be examined.
He has publicly highlighted Arsenal manager Arsene Wenger avoiding sanctions for pushing him in the technical area in October 2014 and for calling referee Mike Dean "weak and naive" following the Gunners' loss at Stamford Bridge last month.
Source : PA