Fenerbahce played in the Under-19 team's match against rivals Galatasaray in the Turkish Super Cup, but the young team left the pitch after a minute to protest against the alleged unfair treatment.
Fenerbahce had requested a postponement of their match to face Greece's Olympiakos in the Europa League quarter-finals on Thursday.
Football authorities rejected this plea.
Mauro Icardi's goal gave Galatasaray the lead, but their opponents abandoned the match.
The match was called off and Galatasaray celebrated winning the Super Cup.
“The time has come for a reset in Turkish football,” Fenerbahce president Ali Kok said at a press conference early Sunday.
Fenerbahçe issued a statement following the canceled match, saying the club had played the game “not to win, but to defend the truth,” adding that it would “continue to stand tall.”
Fenerbahce had asked for a foreign referee to officiate the match, citing unfavorable treatment from Turkish referees.
This comes just days after the Turkish Football Federation suspended two Fenerbahce players for one match. The sanction was imposed following accusations from Trabzonspor fans. He stormed onto the pitch and fought with Fenerbahce players. During the league match on March 17th.
Fenerbahce considered leaving the Turkish Super League, but the members voted against I'll do that.
Sunday's match was played in Sanliurfa, about 1,000 kilometers from both teams' home base in Istanbul, which was hit by a devastating earthquake last year.
Proceeds from the game were donated to victims of the earthquake that claimed over 53,500 lives.
The Super Cup was originally scheduled to be held in Riyadh in December. but it was postponed when Saudi Arabian organizers refused to allow players to wear warm-up shirts with an image of Mustafa Kemal Atatürk, the founder of modern Turkey;