The 29-year-old mixed martial artist appeared in court for no more than two minutes, just one mile away from Barclays Center, where he threw a hand truck at a UFC bus in April.
McGregor's legal team and the Brooklyn District Attorney's Office said negotiations for a potential plea deal are ongoing. The Dublin native's next court date has been scheduled for July 26.
"I regret my actions that led to today," McGregor told a throng of media members outside the courthouse after the hearing. "I understand the seriousness of this matter and I am hopeful this will get worked out."
McGregor and co-defendant Cian Cowley remain free on bail.
McGregor is facing 12 total charges for his involvement in an incident on April 5. Video caught McGregor storming into the loading dock of Barclays Center and attacking a bus full of UFC athletes. He is facing three counts of misdemeanor assault?and one count of felony criminal mischief.
McGregor (21-3) has not fought in the UFC since November 2016. He made his professional boxing debut against Floyd Mayweather last August.
UFC president Dana White told TMZ on Wednesday that he is scheduled to meet McGregor on June 18. Sources have told ESPN the UFC wants to have that meeting in Las Vegas.
Audie Attar, McGregor's agent, told ESPN on Thursday that the team will focus on this legal matter first, before addressing any future fights.
"Today we were here to focus on the court. We're not going to focus on any future plans until we handle this matter," Attar said. "Right now we're in negotiations with the district attorney. We'll focus on that and focus on the future later."
McGregor's attack was allegedly aimed at current UFC lightweight champion Khabib Nurmagomedov (26-0), who had confronted one of McGregor's teammates, Artem Lobov, earlier that week. Nurmagomedov is expected to fight later this year.
According to agent Ali Abdelaziz, Nurmagomedov, of Dagestan, wants to fight former welterweight and middleweight champion Georges St-Pierre next, but the UFC wants to put together a 155-pound fight with McGregor.
"It's sad we have to wait to see if this guy is going to jail or not," Abdelaziz told ESPN. "Khabib wants to fight Georges St-Pierre for his legacy, but the UFC wants the Conor fight. He does not believe Conor deserves to fight for the title, but he is willing to humble him."