The charge relates to the League One play-off semi-final first leg between the two clubs at the Proact Stadium last week.
A testy beginning to the match finally boiled over in the 28th minute when Chesterfield winger Gary Roberts and Preston forward Paul Gallagher tangled.
Roberts appeared to grab his opponent by the throat as both players attempted to get up from the ground and a melee ensued involving men from both sides.
In addition, Preston assistant manager Glynn Snodin has been charged with misconduct.
A statement on the FA’s website said: “Both Chesterfield and Preston North End have been charged by the FA in relation to their Football League One play-off match on 7 May 2015.
“It is alleged that in or around the 28th minute of the fixture, the clubs failed to ensure their players conducted themselves in an orderly fashion.
“In relation to the same game, Preston assistant manager Glynn Snodin has been charged for misconduct in that it is alleged his behaviour during the first half of the match amounted to improper conduct.
“Both clubs and Mr Snodin have until 6pm on 15 May 2015 to respond to the charges.”
Preston won the game in question 1-0 but the second leg of the semi-final at Deepdale on Sunday also courted controversy.
A 3-0 victory saw North End progress to the Wembley final later this month but after the game Chesterfield defender Ian Evatt reported he had been “punched, kicked and spat on” after home supporters invaded the pitch in celebration.
Lancashire Police has since said that a man has been charged in connection with the assault.