Referee John Beaton cautioned the head coach during the 3-2 loss to John McGlynn’s side and showed him a second yellow after the game.
The actions have brought about an SFA notice of complaint for misconduct, and a hearing date set for the middle of next month.
Neilson explained his side of the two incidents after the match: “Part of the reason I got a second yellow was because I just tried to speak to the referee,” he said. “Most referees you are allowed to speak to but he just tells you to get out of his face.
“If you don’t get out of his face then he will yellow-card you. I’m disappointed as I just wanted to speak to him.”
The earlier caution was for complaints made during the game as Hearts fell 3-0 behind before pulling two goals back through Liam Boyce. Neilson was unhappy with some decisions, including the penalty award for Raith’s second goal and an alleged handball at their third.
The Hearts boss will be cited for allegedly breaching the governing body’s rule 203 which states ‘no member of team staff shall commit misconduct at a match’. He will be able to state his case at the hearing, in front of an SFA disciplinary panel, to take place on February 18.
In other disciplinary news, Rangers’ Alfredo Morelos faces a fast-track tribunal for an alleged stamping incident with Hibs’ Ryan Porteous during the sides’ Scottish Premiership encounter at Easter Road this week.