The trio face disciplinary action for their behaviour during and after Saturday's 2-1 home defeat against Sunderland, a result that put a significant dent in Chelsea's Premier League title hopes.
Mourinho faces scrutiny following his post-match comments, when he spoke to "congratulate" referee Mike Dean for his "unbelievable " performance at Stamford Bridge, which the FA allege has called into question the integrity of the official.
Chelsea were sent crashing to defeat when Dean awarded a late penalty that was converted by Fabio Borini after he adjudged Chelsea defender Cesar Azpilicueta to have fouled Jozy Altidore in the area with eight minutes remaining.
It is the second time this month that Mourinho has been charged by the FA, and third this season. He was sent to the stands by referee Chris Foy after entering the field of play during Chelsea's 1-0 loss at Aston Villa last month and was subsequently fined £8,000 for his conduct.
Midfielder Ramires' charge relates to an off-the-ball incident when he clashed with Sunderland midfielder Sebastian Larsson.
The incident, in which Ramires appeared to elbow his opponent, was not seen by the referee, but a three-man panel of former elite officials were unanimous that it was an act of violent conduct.
Faria faces two counts of misconduct for abusive and/or insulting words towards the referee and improper conduct.
The 38-year-old was outraged by the penalty decision and had to be restrained by Mourinho when asked to leave the technical area after angrily confronting the fourth official.
Faria's case was designated as a non-standard case by the FA due to the "aggressive and/or threatening and/or serious nature of the reported behaviour."
Ramires has until 6pm on Thursday to respond to his charge, while Mourinho and Faria have until 6pm on Monday.
