Everton have been charged over the pitch invasions which marred their Premier League match against Crystal Palace on 19 May.
Supporters came on to the field at Goodison Park after the 3-2 victory over the Eagles guaranteed the Toffees' top-flight survival, and one became involved in an altercation with Palace manager Patrick Vieira.
The Football Association said on Monday that the Merseyside club had been charged with two breaches of its rules.
A statement from the governing body read: "It is alleged that in the 84th minute and then following completion of the fixture, Everton FC failed to ensure that its spectators, and all persons purporting to be its supporters or followers, conducted themselves in an orderly fashion and refrained from using threatening and/or violent behaviour whilst encroaching onto the pitch area."
The FA said Everton had until next Monday - 18 July - to respond to the charges.
Similar charges have been issued against Huddersfield and Bristol Rovers after end-of-season incidents.
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