The Chelsea skipper was acquitted of a racially aggravated public order offence by the Westminster Magistrates Court earlier this month but the FA have decided to lay a charge on the defender.
Terry is free to play for England while the inquiry into the incident, which occurred on October 23 last year, continues and has until next week to respond.
"After seeking advice from an external Independent QC, and having considered the evidence and Magistrates' Court decision in the John Terry case, The FA has today charged the Chelsea player following an alleged incident that occurred during the Queens Park Rangers versus Chelsea fixture at Loftus Road on 23 October 2011," read an FA statement.
"It is further alleged that this included a reference to the ethnic origin and/or colour and/or race of Anton Ferdinand.
"This charge is the result of The FA's long-standing enquiries into this matter, which were placed on hold pending the outcome of the criminal trial, and relates to rules governing football only.
"During this period John Terry remains available to play for England.
"Terry has until 3 August 2012 to respond.
"The FA will make no further comment during this time."