Hull substitute Boyd clashed foreheads with England international Joe Hart during a furious exchange in City's 2-0 win at the KC Stadium.
The incident was not seen by referee Lee Mason, but replays suggested Boyd spat at Hart - although Hart said after the game he did not feel he had been spat at by Boyd.
"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 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."
FA Rule E1 [a] governs misconduct - a typical ban for spitting is three games. Wigan defender Antolin Alcaraz received that sanction in November 2011 following an incident against Wolverhampton Wanderers.
City goalkeeper Hart will face no further action having been booked by Mason for his involvement and the FA has confirmed that - in line with the governing body's own rules - it considers the goalkeeper to have been dealt with.
The flashpoint occurred when Boyd was denied a penalty after claiming to have been fouled by Hart.
It has not yet been decided whether City captain Vincent Kompany could face further disciplinary action for his reaction to his sending off in the fiery contest.
Kompany was dismissed just 10 minutes into the game for a professional foul on Hull forward Nikica Jelavic.
That offence carries a mandatory one-match ban but Kompany angrily kicked a wall as he headed down the tunnel and made what could be interpreted as an offensive gesture towards fourth official Anthony Taylor.
The FA could act if these matters are mentioned in reports by the officials.
Any extension to Kompany's suspension would rule him out of the derby against Manchester United at Old Trafford on March 25.
Chelsea manager Jose Mourinho was also waiting to learn whether he might be in disciplinary trouble after he was sent to the stands late in his side's 1-0 loss at Aston Villa.
Mourinho was punished by referee Chris Foy after he, opposite number Paul Lambert and a number of coaches entered the field when a melee broke out following a red-card tackle by Chelsea's Ramires on Karim El Ahmadi.
The role of a number of players might also be examined.
- Sports & Recreation
- George Boyd
- Manchester City
- Vincent Kompany