Boyd has until 6pm on Wednesday to respond to the charge, which relates to an incident which was not seen by referee Lee Mason during the Tigers' 2-0 Barclays Premier League defeat by City at the KC Stadium on Saturday.
An FA statement said: "Hull City's George Boyd has been charged by the FA following his side's game against Manchester City on March 15, 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 March 19, 2014 to respond to the charge.
"Under a new pilot project in Premier League matches this season, if an incident has not been seen by the match officials, a three-man panel of former elite referees will be asked by the FA to review it and advise what, if any action, they believe the match referee should have taken had it been witnessed at the time.
"For an FA charge to follow, all three panel members must agree it is a sending-off offence. In this instance, the panel were of the unanimous decision that it was an act of misconduct."
1 Chelsea 66
2 Liverpool 62
3 Arsenal 62
4 Man City 60
5 Tottenham 53
6 Everton 51
7 Man Utd 48
8 Southampton 45
9 Newcastle 43
10 A Villa 34
11 Stoke City 34
12 West Ham 31
13 Hull City 30
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17 C Palace 28
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20 Fulham 24