Mourinho, who is appealing against a £50,000 (€70,000) fine and suspended one-match stadium ban for comments made about officials following the October 3 loss to Southampton, faces further charges after being sent to the stands by referee Jonathan Moss during the ill-tempered derby at Upton Park on Saturday.
A statement from the FA read: “Jose Mourinho has been charged with misconduct in relation to his language and/or behaviour towards the match officials in or around the dressing room area at half-time.”
He has until 6pm on Thursday to respond to the charge.
A crucial five days awaits Mourinho as Chelsea continue the defence of the Capital One Cup with their manager’s position under intense scrutiny.
Chelsea are looking to respond from a fifth Premier League loss from 10 games this season, in an ill-disciplined clash at West Ham, when they play at Stoke in the fourth round of the Capital One Cup tonight.
Then Jurgen Klopp’s Liverpool visit Stamford Bridge in a match which could be decisive in determining the future of Mourinho, whose side won the League Cup on March 1 and Premier League title on May 3.
Asmir Begovic is expected to continue in goal, although Marco Amelia was on the substitutes’ bench at Upton Park following his free transfer arrival.
If Begovic plays, it would mark his first return to Stoke since his summer switch.
The Bosnia goalkeeper believes Chelsea have been improving but have also been unfortunate, with Cesc Fabregas having a goal ruled out for offside and Kurt Zouma denied by goal-line technology at West Ham.
“We got unlucky with the sending-off,” Begovic said.
“It’s coming from all corners at the moment so we have to cope with that.
“We came back, we showed good character and I think our performance showed we are still positive and trying hard, it’s just that little moments are not going our way.
“I think we had a good goal disallowed as well, so things are just not going for us at the moment. I thought we were well in the game, no matter what the situation was, and the tiny little differences didn’t go our way.
“This league is very unpredictable so we need to take care of our performances first — I think our performances are getting better so we just need to keep that going.”
The events at Upton Park prompted the latest in a long line of disciplinary events involving Mourinho during his second spell as Chelsea boss.
Silvino Louro, one of Mourinho’s assistants, was sent to the stands after Nemanja Matic was sent off for two bookable offences 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.
Chelsea were already hit with an automatic fine of £25,000 (€35,000) for six or more bookings in the contest, while Serbia midfielder Matic will serve a one-match ban, missing tonight’s trip to the Britannia Stadium.
After Mauro Zarate’s opening goal, Chelsea felt a succession of decisions went against them.
Kurt Zouma had a header cleared off the line, with only goal-line technology proving no goal had been scored, before Matic was booked for hauling down Cheikhou Kouyate as he led the counterattack.
Next Cesc Fabregas thought he had scored from Willian’s pass, only to be adjudged offside. It was a decision which infuriated Mourinho, who made his displeasure known to officials.
Matic was then shown a second yellow card for a touchline foul on Diafra Sakho. Louro was sent off and, when Mourinho did not emerge on the touchline for the second half — instead being found in the West Ham directors’ box — it became apparent that he, too, had been dismissed at the interval.
Mourinho afterwards did not speak to the media, in breach of Premier League regulations. But the likely fine is the least of his worries.
However, there was some respite as Bayern Munich boss Pep Guardiola played down rumours that he could replace Mourinho as Chelsea manager.
The Catalan has yet to sign an extension to his current contract with the German champions, which is due to expire at the end of the season, prompting speculation Chelsea owner Roman Abramovich may try to tempt the former Barcelona boss to Stamford Bridge.
However, Guardiola has played down speculation regarding his future. He said: “It’s only October. “We’ve got seven months to work.”
Mourinho has also been backed by Stoke boss Mark Hughes who backed the Chelsea boss to turn things around.
Hughes said: “It’s a period he has the knowledge and understanding to address, and he’ll turn it around. I don’t think anyone thinks that he won’t.
“Chelsea have quality right throughout the club that will enable them to come through this moment I’m sure. He says it himself — he’s a top manager and he’s the best manager Chelsea have ever had, so why would they change?”