He then approached Arsenal's players with his arms aloft before stewards escorted him off the pitch. The man was later arrested.
"Arsenal FC has been charged with breaches of FA Rule E20(a)and (b)," the FA said in a statement.
"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."
Arsenal have until March 22 to respond to the charge.
Pitch invasions in England and Scotland over the weekend have raised fears for player safety, with those in the game warning of potential tragedy unless firm action is taken to tackle the problem.
Before the incident at Arsenal, Aston Villa's Jack Grealish was punched in the face by a man in a Championship (second tier) game at local rivals Birmingham City, while in Scotland, Rangers captain James Tavernier was attacked at Hibernian.
(Reporting by Rohith Nair in Bengaluru, Editing by Simon Jennings)
