The Manchester United footballer was charged in relation to a tweet about Chelsea player Ashley Cole.
Rio had replied to a message suggesting Ashley Cole would be a "choc ice" in the trial of John Terry, who was accused of racially abusing Rio's brother Anton.
He has requested a personal hearing over charge, and has denied any wrongdoing.
An FA statement read: "Manchester United's Rio Ferdinand has today [Thursday, August 2] denied an FA charge of improper conduct in relation to comments posted on Twitter.
"The allegation is that the player acted in a way which was improper and/or brought the game into disrepute by making comments which included a reference to ethnic origin and/or colour and/or race.
"The player has requested a personal hearing."
Rio had previously denied that the tweet was racist, saying: "What I said yesterday is not a racist term. Its a type of slang/term used by many for someone who is being fake. So there."
Arsenal footballer Emmanuel Frimpong was recently fined £6,000 by the FA over comments he made about a Tottenham fan on Twitter.