The West Bromwich Albion striker faces a minimum five-match ban for making what is described as an inverted Nazi salute that has anti-semitic connotations.
Nicolas Anelka, who denies he intended to be anti-semitic, made the salute after scoring in the 3-3 draw against West Ham on 28 December.
The FA brought in an expert to help decide on whether charges should be brought and has spent several weeks working on the case due to its sensitivity.
It said in a statement that it was alleged that “Anelka made a gesture which was abusive and/or indecent and/or insulting and/or improper”.
It added that it was also alleged that “this is an aggravated breach … in that it included a reference to ethnic origin and/or race and/or religion or belief”.
Anelka, who is French and a Muslim convert, has until 6pm on Thursday to respond to the charge.
A three-person independent regulatory commission will now be appointed to deal with the case, either to decide on the sanction if Anelka admits the charge or to hold a disciplinary hearing if he denies it.
On Monday, the property website Zoopla pulled its shirt sponsorship from West Brom because of the incident.
The company, which is co-owned by Jewish businessman Alex Chesterton, had said Anelka should not be selected to play, but he was chosen for Monday night’s clash with Everton.
The “quenelle” gesture was made famous by French comedian Dieudonné M’bala M’bala, who has been fined for hate speech in the past. Anelka said he made the salute as a “dedication to his comedian friend”.
The comedian has been convicted seven times for anti-semitic remarks and paid out thousands of euros in fines.
Dieudonné has had his shows banned in Paris and has made public appearances with former National Front leader Jean Marie Le Pen, who is godfather to his third child.
Anelka’s salute was condemned as a “shocking provocation” by France’s Sports Minister Valerie Fourneyron.