Mourinho was charged on Monday evening over his comments to the media following his side's 3-1 defeat to Southampton in the Barclays Premier League at Stamford Bridge on Saturday which left them in the unaccustomed position of 16th in the table.
Mourinho had earlier on Monday received the backing of the club amid a drop in form which has seen his team go from champions to hovering just above the relegation zone in a matter of months.
What made it worse for Mourinho was Saturday's defeat, a fourth in eight Premier League fixtures this season, came in front of owner Roman Abramovich.
To make matters worse for the under-pressure manager, he has also been charged by the FA over his comments about referee Robert Madley
In a statement on Monday the FA said it had charged the Chelsea boss who was unhappy at the decision not to award a penalty when, with the scores at 1-1, forward Radamel Falcao was upended by Saints goalkeeper Maarten Stekelenburg
The statement read: "Jose Mourinho has been charged for misconduct in relation to media comments he made following Chelsea's game against Southampton on Saturday 3 October 2015.
"It is alleged his remarks constitute improper conduct in that they allege and/or imply bias on the part of a match official or match officials and/or bring the game into disrepute.
"He has until 6pm on Thursday 8 October 2015 to respond to the charge."
Mourinho had said after the Southampton defeat: "When everything goes against you, you need these decisions
One thing teams are not afraid of is to make penalties against us because they make them all the time and the referees they never give.
"It is a big confidence they feel because they are not afraid to be aggressive in the box.
"I tell my players to be careful in the box
These opponents know that they don't have to feel that pressure."
Earlier on Monday Chelsea had expressed their confidence in Mourinho with a statement of their own on the official club website which read: "The club wants to make it clear that Jose continues to have our full support
"As Jose has said himself, results have not been good enough and the team's performances must improve.
"However, we believe that we have the right manager to turn this season around and that he has the squad with which to do it."
Source : PA