The Dutchman was charged by the FA six days ago for remarks made after his side's 0-0 draw at The Abbey Stadium on January, which prompted a replay that Van Gaal's men won 3-0.
Following the stalemate Van Gaal told reporters: "Every aspect of the match is against us - the pitch, the referee. Everything that you can think about this is against you."
Van Gaal revealed last Friday that he would contest the charge, and the FA have now confirmed that he has done so and requested a personal hearing.
A statement posted on the FA's Twitter account read: "Louis Van Gaal denies FA misconduct charge in relation to media comments and requests personal hearing, date to be confirmed.
"The Man Utd manager was charged following The FA Cup tie against Cambridge United on 23 Jan 2015. It is alleged his comments constitute improper conduct in that they allege and/or imply bias on the part of the match referee and/or bring the game into disrepute."
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