Balotelli uploaded on Instagram a picture of the video-game character Super Mario, with whom the Italy international shares a nickname, with text around the image including "jumps like a black man and grabs coins like a Jew."
The striker, who has been subjected to racial abuse on numerous occasions, posted the image of the computerized character on Monday with the heading "Don't be a racist."
However, the FA alleges that the post was "abusive," ''insulting" and "improper," adding that it is an "aggravated breach" of FA rules.
Balotelli has until Dec. 15 to respond to the charge.
The Italian's message also read: "Be like Mario. He's an Italian plumber, created by Japanese people, who speaks English and looks like a Mexican."
Balotelli tried to defend the post as criticism began to intensify online by writing on Twitter: "My Mom is jewish so all of u shut up please." He soon deleted the image from his Instagram account and said on Twitter that he apologized he had offended anyone.
Balotelli is currently sidelined with a groin injury.