Following the trial, in which Chelsea and England defender Terry was acquitted of racially abusing Ferdinand's younger brother Anton, Rio responded to a Tweet that described Chelsea defender and defence witness Ashley Cole as a "choc-ice".
The term is commonly understood to mean "black on the outside, white on the inside".
It was a reference to Cole's testimony in court, in which he said he never heard Terry make a racist remark to Anton Ferdinand during the match in question, between Queens Park Rangers and Chelsea, at Loftus Road last October.
"The FA has today charged Manchester United's Rio Ferdinand with improper conduct in relation to comments posted on Twitter," said an FA 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."
Terry was found not guilty earlier this month after a five-day trial at Westminster Magistrates Court but the FA has since charged Terry in relation to the same case.