The clubs are accused of failing “to ensure their players conducted themselves in an orderly fashion” during their 1-1 draw at Swansea’s Liberty Stadium on December 9.
The charge relates to a confrontation late in the game between Hull pair Tom Huddlestone and Yannick Sagbo and Swansea centre-backs Ashley Williams and Chico Flores.
Sagbo and Williams were both booked, while Swansea midfielder Jonjo Shelvey was also cautioned in the aftermath of the incident.
“Both Swansea City and Hull City have been charged by the FA in that they failed to ensure their players conducted themselves in an orderly fashion in or around the 80th minute of their fixture on December 9, 2013,” read a statement on the FA website.
The clubs have until 6 pm local time on Tuesday to respond to the charge.