The trial begins two weeks after the resignation of the Turkish Football Federation (TFF) chairman and his two deputies over the TFF's failure to agree on how to punish clubs caught up in the scandal.
European football's ruling body UEFA will watch proceedings closely, having increased pressure on the federation to act. Sanctions against clubs could include relegation.
However, the court case concerned only individuals, judge Mehmet Ekinci told the court room, saying: "It's not the teams or Turkish sports we are judging here."
The town has become synonymous with Turkey's murky underbelly as generals and journalists accused of plotting coups are being held at the high-security prison there.
Outside the court, some 2,000 Fenerbahce fans chanted in support of their club's chairman. A tent was set up to serve tea, coffee and soup to them.
"We are right, we will win," they chanted. Fans from Sivasspor and Orduspor were also evident among the crowd.
"Our love is not just for February 14, it will last for ever," said a Fenerbahce banner, alluding to Valentine's Day.
"No criminal record until coming here," said Yildirim, wearing a blue suit and a tie in Fenerbahce's blue-and-yellow colours. He looked through documents and talked with his lawyers in the front row of the defendants' section.
The first four days of the case were set to be taken up by the reading of the 400-page indictment which refers to 13 matches, including Fenerbahce's 4-3 victory over Sivasspor which allowed them to clinch the league championship on the final day of last season.
The federation excluded Fenerbahce from this season's Champions League, with runners-up Trabzonspor taking their place, in an initial move after the investigation started. However, clubs have failed to agree on other disciplinary measures.
"They say I paid Ibrahim Akin 100,000 euro. From which account? Let them prove that and I'll jump off a bridge," media reports quotes Yildirim as saying during a court break.
