U.S. federal judge Richard Berman dismissed the bail application at a courthouse in Manhattan in New York City, citing potential dangers Epstein could pose to the community, especially to his accusers.
Prosecutors also said that Epstein's wealth and resources could help him flee the country if he got bailed out.
Epstein, 66, was accused of sexually exploiting and abusing dozens of underage girls in early 2000s. Prosecutors said he had lured those girls to his homes in New York and Florida and paid them for sex acts and for recruiting more victims.
He faces up to 45 years in prison if convicted.
The former hedge fund manager had avoided federal prosecution 11 years ago on similar charges in Florida by pleading guilty to state charges under a plea deal, which spared him from a lengthy jail time.
The new indictment re-generated public outrage over Epstein and his previous trial. U.S. Secretary of Labor Alex Acosta, who acted as Epstein's lawyer in 2008 and handled the plea deal, was compelled to resign last week amid the furor.