The 30-year-old allegedly swung his right arm at a fan in the crowd after the supporter threw the ball at him before a throw-in during Crawley's 1-0 defeat.
A statement from the FA said: "Crawley Town's Paul Connolly has been charged by the FA following his side's game against Brentford FC on April 8, 2014.
"The charge is in relation to an alleged violent conduct offence involving a spectator. The incident was not seen by the match officials but caught on video.
"The FA has also submitted that the standard punishment of a three-match suspension would be clearly insufficient given the nature of the offence."
Connolly has until 6pm today to respond to the charge.