Chelsea have been charged for failing to control their players during the 2-0 defeat away at Manchester United on Sunday.
Assistant boss Steve Clarke has also been charged with using abusive and/or insulting words towards officials.
Chelsea were incensed by referee Mike Dean's decision to send off Nigerian midfielder Mikel Jon Obi in the first half for a challenge on Patrice Evra.
In a statement, Chelsea announced: "Chelsea Football Club will be strongly defending the two charges issued by the Football Association today and will be considering that defence until we have to respond on October 12."