The FA launched an investigation following an incident involving Charlton forward Jonathan Leko during the game between the two Championship clubs at The Valley on September 28.
Casilla has now been charged with a breach of FA Rule E3, with the governing body giving the Spaniard until November 12 to provide a response.
"It is alleged that, contrary to Rule E3(1), the Leeds United goalkeeper used abusive and/or insulting words towards a Charlton Athletic player during an EFL Championship fixture on 28 September 2019," a statement from the FA read.
"It is further alleged that the words constitute an "Aggravated Breach", which is defined in Rule E3(2), as they made reference to race and/or colour and/or ethnic origin."
Leeds followed the announcement by releasing a short statement of their own, confirming Casilla denies the allegation and will continue to be considered for selection while he awaits a personal hearing.
"Kiko strenuously denies the allegation and has proactively worked with the FA during their investigation to date," the Yorkshire club said.
"The next step of this process will be a personal hearing, in the meantime Kiko will remain available for selection."