Assistant manager Rui Faria has admitted two misconduct charges and requested a non-personal hearing.
Sunderland, who were at the time bottom of the table, ended Mourinho's 77-match unbeaten home league run at Stamford Bridge with a 2-1 win on April 19.
Mourinho could not hide his anger afterwards behind a sarcastic appraisal of the officials.
He has requested a non-personal hearing in the case, the FA has announced.
His assistant Faria, who was dismissed for angrily confronting the match officials, has admitted two charges of misconduct and requested a non-personal hearing.
Midfielder Ramires received a retrospective four-match ban, ending his domestic season, for striking Sebastian Larsson during the loss.
Speaking after the Black Cats match, Mourinho said: "Mike Dean's performance was unbelievable and when referees have unbelievable performances it's fair to congratulate them.
"He came here with one objective, the objective to make a fantastic performance and he did that.
"Congratulations to Mike Riley, because he's the referees' boss, and what they are doing during the whole season is fantastic, especially in the last couple of months, especially in matches involving the teams that were in the title race - it's absolutely fantastic."
An FA statement read: "Jose Mourinho has denied an FA charge and requested a non-personal hearing in relation to comments he made following Chelsea's game against Sunderland on April 19, 2014.
"It is alleged that Mourinho's post-match comments constitute improper conduct, in that they call into question the integrity of the referee appointed to the above fixture (Mike Dean) and/or the integrity of Mr Mike Riley, general manager of the Professional Game Match Officials Limited, and/or the comments bring the game into disrepute.
"In relation to the same fixture, Chelsea assistant manager Rui Faria has admitted two misconduct breaches and requested a non-personal hearing.
"The first breach was that Faria used abusive and/or insulting words towards the fourth official (Phil Dowd). The second breach was that Faria's behaviour following the match referee's request that he leave the technical area amounted to improper conduct.
"A date for both hearings will be set in due course."
.....Look Jose's comments were about as innocent, selfless and pure as Prince Naseem Hamed's comments were about his opponents at any of his pre- (or post-) fight conferences, ie. not at all. I know, they still should have let him off. "Jose, Jose, Jose.......the World Simply was Not Meant for one as Beautiful As You!" I see Curly & Moe got fingered too !- oioisaveloy