The Arsenal midfielder is alleged to have brought the game into disrepute with tweets that referenced "ethnic origin, faith or race" after an exchange with a Tottenham fan
Frimpong faces the allegation that his comments amounted to improper conduct and/or brought the game into disrepute while including "a reference to ethnic origin, faith or race".
The 20-year-old has until 16:00 on July 27 to respond to the charge, which likely refers to a tweet in which he called a rival Tottenham fan a "Scum Yid".
Frimpong had posted the message "if you going church today Pray For me Giving today A Miss", to which the Spurs fan had replied "I prayed you break your arms and legs".
That comment drew the tweet in question from Frimpong. The term 'yid' is considered offensive by many towards Jewish people but Tottenham fans have embraced the name over the years in an effort to defuse it as an insult towards the club. The term surrounds the club due to the perceived number of Jewish supporters of the north London team.
Comedian and high-profile Chelsea fan David Baddiel, however, launched a campaign to end the use of the term by the club's own supporters.
Frimpong, who spent time on loan at Wolves before a season-ending injury during the 2011-12 campaign, had been reprimanded by Arsenal but now faces official charges.
The FA has been dogged by incidents regarding ethnicity, faith and race over the past year, most notably suspending Liverpool striker Luis Suarez for eight matches after he was alleged to have made offensive comments of a racially aggravated nature towards Manchester United defender Patrice Evra.
Chelsea defender John Terry is currently under investigation by the English footballing body for the alleged racial abuse of QPR defender Anton Ferdinand, although he was found not guilty in a criminal court.