Boyd was involved in an altercation with the England goalkeeper midway through the second half of Saturday's Premier League match at the KC Stadium, which Manuel Pellegrini's men won 2-0.
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Hart was booked for pushing his head into the Hull player's face, yet Boyd's subsequent actions have provoked action from the FA.
A statement from the governing body on Tuesday read: "Hull City's George Boyd has been charged by The FA following his side's game against Manchester City on 15 March 2014.
"The charge is in relation to an alleged breach of FA Rule E1 [a] in that in or around the 68th minute of the game Boyd spat at Manchester City's Joe Hart.
"The incident was not seen by the match officials but caught on video.
"Boyd has until 6pm on 19 March 2014 to respond to the charge."