The 20-year-old fan responded to a Tottenham fan on July 15 and although he shortly removed the comment from the social networking site, it has not escaped the attention of the FA.
"Arsenal's Emmanuel Frimpong has been charged under FA Rule E3 for improper conduct in relation to recent comments made on Twitter," said a statement on the FA's official website.
"The allegation is that Frimpong posted comments amounting to improper conduct and/or which brought the game into disrepute, which included a reference to ethnic origin, faith or race.
"The player has until 4pm on 27 July 2012 to respond to the charge."
It is believed the player will also be fined by his club.