Anelka had until 6pm on Thursday to respond to the governing body's assertion that his goal celebration at West Ham last month was "abusive or indecent or insulting or improper".
The FA further alleged it to be an aggravated breach, in that it included a reference to ethnic origin and/or race and/or religion or belief.
Anelka, who faces a minimum five-match ban if found guilty, has repeatedly insisted the sign - considered by some to have anti-Semitic connotations - was an anti-establishment one without racial intent.
And the FA confirmed shortly after the deadline that the Frenchman intended to fight his case at a forthcoming hearing, a date for which has yet to be confirmed.
West Brom also confirmed Anelka's decision and said they would make no further comment "until the FA's disciplinary process has reached a conclusion".
The 34-year-old, who it is understood will pay his own legal bill, had earlier this week used social media to maintain his defiant stance.
He wrote on his Faceboook page: "I ask that the FA kindly remove the charges alleged against me. And I repeat, I am neither anti-Semitic nor racist."
Anelka has also received the backing of Dieudonne M'bala M'bala, the French comedian who invented the quenelle gesture.
"Nicolas Anelka has all my support, that's evident," he said.
"I consider him a brother in humanity. He's someone who is very courageous and for whom I have very much respect and admiration.
"Anelka is a descendant of slaves and if he wants to remark on this history then he has the right to - and we are all very proud of him doing so."
The striker's defence has, however, found no favour in other quarters, with the Board of Deputies of British Jews citing his apparent lack of remorse.
Vice-president Jonathan Arkush said: "I know under the rules that on a first-time offence there is a minimum five-game suspension but I think what he did was sufficiently serious to justify a longer suspension than five matches.
"He has not indicated one bit of remorse or regret or apologised for his actions. He has simply said he wouldn't do it again and that is not good enough."