Mangione, 27, had pleaded not guilty to federal charges of murder, weapons possession and stalking in connection with the 2024 shooting that shocked New York City and drew nationwide attention.
While the killing was widely condemned by public officials, Mangione emerged as a controversial figure, with some Americans portraying him as a folk hero amid anger over rising healthcare costs and insurance practices, media reports said.
U.S. District Judge Margaret M. Garnett ruled that the murder and weapons charges were legally incompatible with the two stalking counts Mangione still faces under federal law, prompting their dismissal.
Jury selection in the federal case had earlier been scheduled to begin in September.
Mangione, however, is not out of legal trouble. He has separately pleaded not guilty to murder, weapons, and forgery charges in Manhattan state court.
A trial date in the state case has yet to be set.
The ruling marks a significant turn in one of the most closely watched criminal cases tied to corporate leadership violence in recent years.