An FA statment says the Blues failed to control their players at Old Trafford and assistant boss Steve Clarke has also been charged for mouthing off to the match officials.
The FA statement read: “Charges have today been issued against Chelsea FC and the club’s assistant coach Steve Clarke.
“Chelsea have been charged with failing to control their players during their match against Manchester United on September 23.
“This charge relates to the conduct of Chelsea players towards referee Mike Dean following the sending-off of Mikel John Obi.
“Steve Clarke has been charged with using abusive and/or insulting words towards the match officials after the end of the match at Old Trafford.
“Chelsea and Clarke have until October 12 to respond to the charges.”