The Spaniard has been charged under rule E3 which alleges he used abusive and/or insulting words.
Furthermore, the FA has charged Casilla with an aggravated breach, and that his words related to race and/or colour and/or ethnic origin.
Leeds have released a statement in which they say Casilla “strenuously denies the allegation”.
It reads: “Leeds United Football Club acknowledges the charge from the FA today relating to Kiko Casilla and an alleged breach of FA Rule E3 during our Sky Bet Championship match with Charlton Athletic at The Valley in September.
“Kiko strenuously denies the allegation and has proactively worked with the FA during their investigation to date.
“The next step of this process will be a personal hearing. In the meantime, Kiko will remain available for selection.”
FA rules state that from the start of this season, anyone found guilty of an aggravated breach faces a mandatory minimum suspension of six matches, which may be increased based on any additional aggravating factors.
Casilla, who has played every minute of Leeds’ season so far, has until Tuesday November 12 to respond.