Warnock was critical of the display of match referee Craig Pawson after the Premier League loss at Selhurst Park on Saturday.
Pawson sent off Chelsea's Cesar Azpilicueta late in the first half for a rash lunge on Mile Jedinak before the numbers were evened up when Damien Delaney was dismissed for a second bookable offence.
Warnock felt aggrieved that a robust challenge from John Terry on Fraizer Campbell had earlier gone unpunished, as well as believing the Chelsea players had surrounded Pawson and pressured the official into brandishing a second caution to Delaney.
The Palace manager stated in a media conference on Thursday that he expected to be contacted by the governing body, with the FA later confirming that he has been charged and has until October 27 to respond.
"Crystal Palace manager Neil Warnock has been charged by The FA for misconduct in relation to media comments he made after the game against Chelsea on 18 October 2014," an FA statement read.
"It is alleged that Warnock's post-match comments constituted improper conduct in that they implied the match referee was motivated by bias; and/or brought the game into disrepute, in contravention of FA Rule E3[1]."
