This story contains language which you may find offensive.
The 24-year-old reposted an image of computer game character Super Mario on Instagram, which included the words "jumps like a black man and grabs coins like a Jew."
The Italian tweeted to deny the post was offensive, before apologising.
He has until 18:00 GMT on 15 December to respond to the charge.
A Liverpool spokesman said: "We acknowledge the FA's decision and the player will work through the process to answer the charge.
"While that process is on-going the club will make no further comment."
An FA statement read: "It is alleged the Liverpool player breached FA Rule E3[1] in that his posting was abusive and/or insulting and/or improper.
"It is further alleged that this is an 'Aggravated Breach' as defined by FA Rule E3[2] as it included a reference to ethnic origin and/or colour and/or race and/or nationality and/or religion or belief."
Balotelli had until 18:00 on Friday to submit an explanation for his comments to the FA and he reportedly provided evidence of the discrimination he has faced during his career.
The picture posted by the player had an image of Super Mario with the heading: "Don't be a racist!"
The text read: "Be like Mario, he's an Italian plumber, created by Japanese people, who speaks English and looks like a Mexican."
"He jumps like a black man and grabs coins like a Jew."
After receiving criticism on Twitter for the image, Balotelli tweeted: "My mom [sic] is Jewish so all of you shut up please."
He also described reposting the image as "my unlucky moment".
However, he later wrote: "I apologise if I've offended anyone.
"The post was meant to be anti-racist with humour. I now understand that out of context it may have the opposite effect.
"Not all Mexicans have a moustache, not all black people jump high and not all Jewish people love money.
"I used a cartoon done by somebody else because it has Super Mario and I thought it was funny and not offensive. Again, I'm sorry."
Balotelli, who will miss Liverpool's match against Sunderland on Saturday with a groin injury, has scored only two goals in his 14 appearances for the club this season.
Liverpool striker Mario Balotelli has been charged by the Football Association for a post on social media which appeared to contain anti-Semitic and racist references.