A supporter ran onto the field and confronted Manchester United defender Chris Smalling during Arsenal's Premier League match at Emirates Stadium on Sunday just hours after the controversial incident in Birmingham, when a spectator punched Aston Villa's Jack Grealish.
The fan at the Arsenal match entered the field to join in with the Gunners players' celebrations after Pierre Emerick-Aubameyang converted a second-half penalty, shoving Smalling as he ran past him.
Arsenal have until Friday, March 22 to respond to the charge, which relates to breaches of FA Rules E20(a) and (b).
A statement issued by the FA read: "It is alleged the club failed to ensure that its spectator[s] conducted themselves in an orderly fashion and refrained from encroaching onto the pitch during the Premier League fixture against Manchester United on Sunday."
Police arrested a man on suspicion of common assault and pitch invasion, while Arsenal announced their intention to issue a ban.
The fan in question, Gary Cooper, gave an interview to the Daily Mail and apologised for his actions.
"I am just so ashamed and have let myself and my family down. What happened was out of character. I am still in shock and feel awful," he said.
"I got caught up in the emotion of the game and made a foolish mistake to run on to the pitch.
"I had no intention of approaching Chris Smalling. He happened to be there as I ran to congratulate the Arsenal players.
"I am deeply ashamed of my actions and would never do anything to harm any of the players."
Meanwhile, the governing body have charged Championship side Birmingham with the same offence in response to the attack on Grealish.
Paul Mitchell, 27, was jailed for 14 weeks by magistrates in Birmingham for the incident in the local derby, in which the Aston Villa midfielder went on to score the only goal in a 1-0 win for the visitors.
A statement from the FA read: "It is alleged the club failed to ensure that its spectator[s] conducted themselves in an orderly fashion; refrained from improper or violent conduct and refrained from encroaching onto the pitch during the EFL Championship fixture against Aston Villa on Sunday."
Birmingham also have until Friday, March 22 to respond to the charge.