West Ham have been charged after supporters invaded the pitch at the London Stadium during the Premier League defeat by Burnley in March.
Fans repeatedly went onto the pitch during the game, with one approaching Hammers captain Mark Noble and another running on with a corner flag.
Supporters also threw coins and objects as they protested in front of the directors’ box.
The east London club has until 5 July to respond to the charge.
“West Ham has been charged for failing to ensure its spectators conducted themselves in an orderly fashion and that no spectators or unauthorised persons encroached onto the pitch,” the Football Association said in a statement.
Hammers vice-chairman Karren Brady called it “one of the most painful days” in the club’s history.
West Ham gave several fans lifetime bans following the trouble.