The FA say Casilla is alleged to have breached FA Rule E3 by using 'abusive and/or insulting words' towards an opposition player during the Championship clash with Charlton Athletic at The Valley in September.
An FA statement said: "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.
"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.
"Kiko Casilla has until 12 November 2019 to provide a response."
Leeds say the player 'strenuously denies' the allegation and has worked with the FA during the investigation.
He will remain available for selection pending a personal hearing.