West Brom's French striker is facing a minimum five-match ban under new FA rules after the gesture, which some say is an inverted Nazi salute and has anti-Semitic connotations.
Anelka has been charged with making a improper gesture and that it was an aggravated breach, in that it included "a reference to ethnic origin and/or race and/or religion or belief.
Anelka, who has denied the goal celebration was intended to be anti-Semitic, made the quenelle salute after scoring in the 3-3 draw against West Ham on December 28.
The FA said in a statement: "The FA has charged the West Bromwich Albion player Nicolas Anelka following an incident that occurred during the West Ham United versus West Bromwich Albion fixture at the Boleyn Ground on 28 December 2013.
"It is alleged that, in the 40th minute of the fixture, Anelka made a gesture which was abusive and/or indecent and/or insulting and/or improper, contrary to FA Rule E3.
"It is further alleged that this is an aggravated breach, as defined in FA Rule E3, in that it included a reference to ethnic origin and/or race and/or religion or belief."
Anelka has until 6pm on Thursday to respond to the charge.