Cook, 52, is alleged to have verbally abused referee Oliver Langford after Wigan’s 2-2 home draw against Middlesbrough in Tuesday night’s Championship game.
Balogun made his debut in the game, coming on in the second half after Cheyenne Dunkley got sent off.
A statement on the FA Spokesperson’s Twitter site read: “Wigan Athletic FC’s Paul Cook has been charged with two breaches of FA Rule E3 following the EFL Championship fixture against Middlesbrough FC on Tuesday February 11, 2020.
“It is alleged that the manager used abusive and/or insulting words towards the match referee in the tunnel area at the end of the fixture.
“It is also alleged that the manager’s language and/or behaviour in the match officials’ dressing room amounts to improper conduct. Paul Cook has until Tuesday, February 18, 2020 to respond.”
Langford gave out 10 yellow cards during the game, including two which resulted in the dismissal of Dunkley.
Wigan are third from bottom in the 24-team league table, four points from safety.
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