The West Brom striker courted controversy on December 28 when celebrating a goal against West Ham by performing the gesture.
Anelka said the ‘quenelle’ was a show of support for his friend, French comedian Dieudonne M’Bala M’Bala, but it has anti-Semitic connotations.
The FA had been criticised for the length of time it had taken to address the matter but confirmed on Tuesday morning that Anelka had been charged.
A statement read: "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 23 January 2014 to respond to the charge."
If found guilty under the second part of the rule, Anelka will face a minimum five-game ban.
The FA only brings charges when it feels confident of winning the case and the vast, vast majority of cases are proven.
A club statement read: "West Bromwich Albion has noted The FA’s charge against Nicolas Anelka regarding the gesture he made after scoring his first goal against West Ham United on December 28.
"Anelka has received a 34-page document explaining the allegations against him and informing him that he has until 6pm on Thursday to respond. The player is now considering his options.
"Under FA rules, Anelka remains available for first-team selection until The FA’s disciplinary process has reached its conclusion. Following this, the club will conclude its own internal enquiry."
The striker was in the headlines again prior to the club's 1-1 draw at home to Everton on Monday night after club shirt sponsor Zoopla said it would not be renewing its £3 million two-year deal following the furore over Anelka's controversial 'quenelle' gesture.
There were reports the company has requested the forward not be picked but manager Pepe Mel said he made decisions for the good of the team.
Asked whether he considered dropping Anelka, the Spaniard said: "No. We needed to win tonight.
"Nicolas is a very good player. He is a very good professional and I am only the head coach.
"I spoke to him yesterday and asked him if he was ready to play and he said he was.
"My obligation is to think about football and the best interests of West Bromwich Albion.
"If he is suspended then I won't be able to play him but at the club we must just think about winning matches."