The Football Association has charged Bradford City and Millwall with failing to ensure their players conducted themselves in an orderly fashion.
The charge relates to their FA Cup third-round replay, which City won 4-0.
A first-half foul by Lions skipper Alan Dunne prompted a melee between both sets of players that also saw Bradford boss Phil Parkinson and assistant Steve Parkin sent to the stands.
Parkinson and Parkin have also been charged with improper conduct.
They, along with both clubs, have until 18:00 GMT on Wednesday, 21 January to respond to the charges.
After beating Championship strugglers Millwall on 14 January, League One Bradford will face Premier League leaders Chelsea in a fourth-round tie at Stamford Bridge on Saturday.
Millwall chairman John Berylson has offered to refund the 456 Lions supporters who purchased tickets in advance of the match.