After his side were held to a surprise goalless draw with the League Two side at the Abbey Stadium, Van Gaal told reporters that "every aspect of the match is against us".
"The pitch, the referee. Everything that you can think about this is against you," the Dutchman, whose team won the fourth-round replay 3-0, added.
That landed him in hot water with the Football Association, who confirmed the charge in a statement that said his comments "allege and/or imply bias on the part of the match referee and/or bring the game into disrepute".
Speaking on Friday, Van Gaal was asked whether he will appeal, and answered: "Yes of course. Of course.
"You as the media have confirmed it and it's always like that so I said in front of the game, after the game, only in meaning that general feeling of everybody for the underdog.
"You can confirm as media that I never say something about the referee in all the matches I have played.
"When I say that, then I am maybe right to be charged but I don't say it.
"I am not angry, I am very disappointed. I am now for nearly 30 years a trainer-coach or manager and I have never been charged.
"Up to now I don't think I said something wrong.
"I said in the press conference the same phrases, because I know in advance that everything is in favour of the underdog."
United face a trip to Preston North End in the fifth round as they go in search of the club's first FA Cup triumph since 2004.
