Gary Cooper, 30, from Surrey, has been charged with common assault and encroaching on to the pitch.
He was bailed to look in Highbury Corner Magistrates’ Court on 26 March.
The episode happened in the 2nd half of the match in Emirates that Arsenal won 2-0.
Arsenal have until 22 March to respond to the FA charge.
An FA spokesperson said:”It is alleged the club failed to make certain that its spectator[s] ran themselves in an organized fashion and refrained from encroaching onto the pitch throughout the Premier League fixture against Manchester United on Sunday.”
The episode happened the identical afternoon as Aston Villa midfielder Jack Grealish was attacked within a Championship game against Birmingham City.
Birmingham fan Paul Mitchell has been jailed to get 14 weeks after working to the pitch and then hitting Grealish from about 10 minutes in to the match.
City also have been charged by the FA for failing to control their own fans.