The relegation-threatened Black Cats ended Mourinho's 77-match unbeaten home league run 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 Rui 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.
Mourinho and Faria had until 1800BST on Monday to respond to the charges, which were levelled last Wednesday
A 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."
Source : PA
Source: PA