Johnson was sent to the stands by referee Eddie Ilderton in Saturday's 1-0 home defeat to Tranmere for his protests after the visitors were awarded a last-gasp penalty deep into injury time.
Latics goalkeeper Mark Oxley was penalised as he dived to push the ball away from Rovers substitute Ryan Lowe but Johnson was convinced he had got the ball.
He now has until Friday evening to respond to the charge.
An FA statement read: The FA has charged Oldham Athletic manager Lee Johnson for an alleged breach of FA Rule E3 in that his behaviour in or around the 90th minute of his side's game against Tranmere Rovers on 31 August 2013 amounted to improper conduct.
"Johnson has until 6pm on 6 September to respond to the charge."
Speaking after Saturday's match at Boundary Park, Johnson's anger at the penalty verdict was clear to see.
"The penalty was an unbelievable decision. Nobody even appealed," he said.
"You could see by the way I threw my jacket four rows back into the crowd that I didn't agree with it and now, having seen it on video, I haven't changed my mind.
"It's a horrible way to lose, but you can't legislate for that kind of mistake and I suppose I'll face some sort of punishment myself."