The appeal is scheduled to take place at Hampden on May 30 and the relegated Dark Blues say "no further comment will be made until after that appeal is heard".
It is reported that Brown is being probed by the SFA for comments made at his post-match interview at Dens Park on May 5.
Brown was critical of referee Alan Muir, who awarded Aberdeen a penalty which they scored to earn a 1-1 draw and relegate Dundee from the Scottish Premier League.
Aberdeen have since accepted a two-match suspension for midfielder Peter Pawlett for simulation in winning the spot-kick.
An SFA statement had earlier explained that Brown was being cited for: "Making comments in a media interview that criticise a decision and the performance of the match officials in such a way as to indicate incompetence."
The Dark Blues boss also claimed he would quit his post if punished by the SFA for his remarks.