This follows his dismissal in the controversial loss at Aston Villa earlier this month.
Mourinho had until 6pm on Monday to formally address the charges and on Friday intimated he would contest, with the FA understood to now be preparing for a personal hearing.
The Portuguese was sent to the stands by referee Chris Foy in stoppage time of the 1-0 loss at Villa Park after approaching the official.
Mourinho went on to the pitch following a red card being shown to his player Ramires.
It was the second time Mourinho had been sent to the stands this season.
Following his sending-off against Cardiff in October, Mourinho accepted the charge and was fined £8,000.
Chelsea lost 1-0 at Villa Park, with Mourinho dismissed after Ramires had been shown a red card for an over-the-top tackle on Karim El Ahmadi. As well as Ramires, Willian was sent off during the contest.
The Chelsea manager came on to the pitch as a melee ensued involving players from both teams, with the substituted Gabriel Agbonlahor and Villa manager Paul Lambert also on the field of play.
The Portuguese claimed he was only attempting to cool tempers and to ask Foy why he had not sent off Agbonlahor for accosting Ramires, but the referee was not interested and he dismissed the Chelsea manager.
Mourinho also said he asked to speak to Foy in the referee's room, but the request was turned down.
The Blues boss then called on the Premier League not to appoint Foy for Chelsea matches.
Mourinho was still seething at Foy on Saturday, even after the 6-0 defeat of Arsenal, as the loss conceded the initiative in the title race to Manchester City, who have games in hand over the Blues.
Mourinho said: "Can we play against Aston Villa again? No.
"The momentum was broken last Saturday. Somebody broke the momentum and now we are trying to build another momentum."