Supporters encroached on to the playing surface after Will Grigg's goal sealed a famous victory over the Premier League's runaway leaders last month.
Sergio Aguero clashed with one fan on the pitch, although the Argentina international was not charged following the incident .
Both clubs were charged with failing to control their players after a brawl erupted in the wake of Fabian Delph's late challenge on Wigan's Max Power, for which the player was sent off.
And the FA has now confirmed League One side Wigan have been charged over the pitch invasion at the end of the match.
"Wigan Athletic have been charged for failing to ensure that no spectators or unauthorised persons encroached onto the pitch at the FA Cup match against Manchester City on Monday February 19," the FA said in a statement.
"The club has until 18.00 BST on Monday April 9 to respond to the charge."
After knocking City out to reach the FA Cup quarter-finals, Wigan subsequently suffered a home loss at the hands of Southampton to exit the competition.