The Tigers have confirmed that Boyd will challenge the charge, which was made after a three-man FA panel reviewed video evidence.
The Scotland international was alleged to have spat towards Hart as the pair angrily confronted each other after Boyd fell under Hart's challenge in the box.
Hart was booked by referee Lee Mason and as a result he will face no further action.
Boyd is set to receive a three-match ban if he fails to prove his innocence, which could rule him out of the Tigers' forthcoming Barclays Premier League games against West Brom, West Ham and Stoke.
Boyd insisted after his side's 2-0 defeat that Hart should have been sent off, claiming: "He didn't nut me but he's put his head in, so he should have got sent off really."
Video footage later emerged which appeared to show Boyd spitting in Hart's direction, but Tigers boss Steve Bruce launched an impassioned defence of his player.
Bruce said: "George Boyd would not do that, not a chance - not deliberately, anyway. He is as honest as they come."
Manchester City captain Vincent Kompany has already escaped further censure from the FA after appearing to make a gesture towards fourth official Anthony Taylor after his 10th minute sending-off.
Kompany explained his actions to the FA and the governing body confirmed on Tuesday he will face no further action.