QPR's on-loan Tottenham defender was charged following social media posts relating to the 'quenelle' gesture. Hull striker Yannick Sagbo has also been charged, while Samir Nasri and Mamadou Sakho have also been rapped on the knuckles.
The salute came to the fore when West Brom forward Nicolas Anelka made the arm gesture when celebrating a goal against West Ham on December 28.
An independent regulatory commission last month handed down a five-match ban to the former France international after finding it "did contain a reference to anti-Semitism" in that it is strongly associated with his friend, the French comedian Dieudonne M'bala M'bala, who has been convicted seven times of anti-Semitic crimes.
In a statement, Assou-Ekotto said: "I am disappointed to have been charged by the Football Association with misconduct in respect of my use of Twitter but I am grateful that as part of this process I will be able to present my case to them.
"I would like to reassure the fans of both Tottenham and QPR, along with the football community generally, that I condemn discrimination and racism in any form.
"During my seven years as a player at Tottenham, my record of engaging with the diverse local community and my strong stance on anti-racism issues speaks for itself.
"I am proud that the work undertaken by my foundation in educating young people has as its cornerstone inclusion and respect for diversity.
"I will not be making any further comment in respect of these issues whilst the Football Association's disciplinary proceedings are ongoing but would like to thank all of those people who have provided me with messages of support since the charge was confirmed by the Football Association."
West Brom sacked Anelka for "gross misconduct" on March 14 - just hours after he took to Twitter claiming he had decided to terminate his contract - once it was confirmed neither he nor the FA would contest the ban.
The governing body had argued for a more severe sanction and on Tuesday confirmed action against Assou-Ekotto, Sagbo, Nasri and Sakho.