New York state Justice Gregory Carro did not explain why jurors would remain anonymous.
While not the norm in US criminal trials, judges often decide to shield jurors' identities from the public in high-profile cases where there is concern jurors may be subject to harassment or intimidation.
Mangione, 28, is accused of shooting UnitedHealthcare CEO Brian Thompson outside a hotel in December 2024.
The killing was widely condemned by public officials but became emblematic of many peoples' frustration with health insurance industry practices in the United States.
Mangione has pleaded not guilty to murder, weapons and forgery charges brought by Manhattan District Attorney Alvin Bragg.
He also pleaded not guilty to stalking charges in a separate federal case.
Jury selection for the trial is expected to start on September 8.
At Tuesday's hearing, Carro also ruled that an overflow courtroom would be made available for the press and the public to witness the trial if the main courtroom fills to capacity.
Prosecutors say they can prove Mangione's guilt with hundreds of hours of surveillance video, fingerprints, DNA, a mobile phone, a gun with matching ballistics and a notebook in which Mangione allegedly wrote of hating insurers and wanting to kill.
Mangione's lawyers have revealed almost nothing about their potential trial strategy although a July court filing indicated they might argue Mangione lost control of his actions due to an extreme mental health breakdown.
They have not conceded that he was the shooter.
Thompson led UnitedHealth Group's insurance unit before he was shot dead in the early morning outside a hotel where an investor conference was taking place.
Graphic footage of the killing and a five-day manhunt for a suspect made the case a media fixture and social media sensation.
Mangione was arrested in Pennsylvania.
His trial in the federal case is scheduled to begin in January.
