The FA say that his comments following the goalless draw with Cambridge United in January "allege and/or imply bias on the part of the match referee and/or bring the game into disrepute".
The Dutchman had said: "Every aspect of a match is against us - the pitch, the referee, the fans."
But when asked on Frday if he will fight the accusation, Van Gaal replied: "Yes of course, of course. I never said anything wrong.
"You can confirm that as media that I have never said anything about referees, never, in all the matches that I have played. I never say something about the referee.
"I'm not angry, I'm very disappointed. I'm now for nearly 30 years a trainer coach, or manager, and I have been never charged and still up to now I don't think that I said something wrong.
"I said already in our press conference the same phrases, because I know in advance that everybody is in favour of the underdog, you as media have confirmed it, it's always like that.
"So I said it in front of the game, I said it after the game only in the meaning of a general feeling of everybody [going] for the underdog. I cannot imagine that the FA has charged me, but okay it's like
that, so ..."
Van Gaal also answered questions on his team's playing style following criticism from fans and media in recent weeks, and he believes things are going well.
“It is not a question of playing with or without wingers or how many defenders, the playing style must be attractive," the former Barcelona boss added. "We could have played better in ball possession as we are having unnecessary losses in possession.
"We have very good defensive and attacking organisation. We are fourth in scoring goals and also fourth or third in defence. I don’t think we are very bad. We are very good, but we can improve."
