There was a melee after Everton’s James McCarthy tackled Morgan Amalfitano, with a large number of West Ham players confronting the Republic of Ireland international.
Both McCarthy and Winston Reid were booked by referee Mark Clattenburg.
A statement on the FA website read: “Everton and West Ham United have been charged by The FA following their game on 22 November 2014.
“It is alleged that in or around the 40th minute of the fixture, both clubs failed to ensure their players conducted themselves in an orderly fashion.
“The clubs have until 6pm on 1 December 2014 to respond to the charge.”