Flanagan is set to be handed a two-game ban for elbowing Celtic captain Scott Brown in a melee at a second-half corner kick.
The Liverpudlian defender was booked for the incident by referee Kevin Clancy but faces retrospective punishment following the Light Blues’ 2-0 win at Ibrox because the match official said he did not fully see the coming-together.
Celtic defender Simunovic, however, escaped any penalty despite colliding with Jermain Defoe off of the ball in the first half.
It has been claimed the SFA’s disciplinary panel could not reach a unanimous decision on the Simunovic incident and that therefore, he will not be reprimanded.
But Rangers have reacted strongly to Flanagan’s notice of complaint from SFA compliance officer Clare Whyte and insist that they have received unfair treatment.
This was the second successive Old Firm showdown to be filled with flashpoints after a meeting at Parkhead in March saw Alfredo Morelos sent off the in the first half, Andy Halliday dismissed after half time and Ryan Kent handed a retrospective two-game suspension.
All three clashes came with Celtic midfielder Brown but the Hoops skipper was not punished despite provoking the Rangers players by celebrating in front of the away fans after the full-time whistle sealed a 2-1 win for his side.
And in a furious statement, Rangers insist the treatment they have received is not just.
The Gers told the Press Association Sport: “Once again, there seems intent to change the decision of a referee in a match involving Rangers.
“There seems to be a steady erosion of respect for Scotland’s referees and the authority they are meant to enjoy under rule five of the laws of the game.
“The decisions of referees regarding facts connected with play are meant to be final, but referees are now routinely invited to change their decisions after a game has finished.
“It is particularly shocking that another Rangers player has been singled out for retrospective action and issued with a notice of complaint, while Jozo Simunovic, the Celtic player who used an elbow to fell Jermain Defoe, has escaped any kind of censure.
“Why did one incident escape punishment while the other is now deemed worthy of a red card?
“We cannot understand how these two incidents could be studied yet only one be considered worthy of punishment.
“It seems as if Rangers’ players are being held to a different code of conduct from players at other clubs.
“We shall vigorously defend Mr Flanagan and have also asked for full transparency on what matters are brought forward for retrospective action. Are those decisions being made even-handedly?”
Flanagan is expected to miss out on the final match of the season against Kilmarnock at Rugby Park on Sunday (3pm) as well as the first game of next season.
A hearing will be held tomorrow at Hampden as Rangers seek to overturn the decision.