The centre-back is accused of bringing the game into disrepute following a message on the social networking site, in which he referred to Chelsea's Ashley Cole as a "choc-ice"
The charge is believed to relate to the aftermath of John Terry's race trial, at which he was acquitted, when Ferdinand quoted a tweet calling Chelsea left-back Ashley Cole, who was a witness for the defence, a "choc-ice".
The term was in reference to Cole's testimony in court, in which he said that he did not hear Terry make a racist comment to Anton Ferdinand, brother of Rio, during the Blues' match against QPR last October at Loftus Road.
Ferdinand later defended his remark on Twitter, stating: "What I said is not a racist term. It is a type of slang [or] term used by many for someone who is being fake. So there."
The FA said in a statement: "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."
Ferdinand will have until Thursday to answer the charge.
Terry was also charged by the FA with improper conduct last week for the original comments made to Anton Ferdinand, which the Chelsea captain immediately declared that he would contest.