The Football Association has charged Fulham following the trouble that marred last season's home victory against Chelsea.
Cottagers fans spilled on to the pitch at the final whistle to celebrate the 1-0 win on 19 March, but matters turned ugly when visiting supporters also ran on to the Craven Cottage turf.
The club have been charged for their alleged failure to ensure that all persons purporting to be its supporters or followers conducted themselves in an orderly fashion and refrained from violent and/or provocative behaviour.
The FA has also charged Fulham with their alleged failure to ensure that no spectators were permitted to encroach onto the pitch area.
The club have until 5 September to respond to the charges.
In the aftermath of the game the FA's chief executive Brian Barwick said: "The FA condemns the behaviour of the mindless individuals who invaded the pitch post-match at Craven Cottage.
"We will be launching a full investigation - with immediate effect - working closely with the police, clubs and media.
"Once identified, the FA would expect the fans concerned to face police charges and banning orders to be sought. The scenes were unacceptable, we all must continue to work hard in this area.
"Thankfully, these kinds of incidents are few and far between these days and that is due to the increased vigilance of our game.
"It is also why behaviour of this nature must be treated seriously and swiftly - sending a clear message to those involved that their actions will not be tolerated."