Portsmouth have been charged by the FA following the pitch invasion after their win over Barnsley in April.
The home fans charged onto the pitch after beating the Reds 3-2, with two late goals, to clinch promotion and the League One title.
Footage appeared to show Barnsley defender Jamie McCart being struck in the head by a fan.
The FA say Portsmouth failed to ensure their supporters and spectators conducted themselves in an orderly fashion on the night. They have until June 7 to respond.