Epstein was arrested at an airport in New Jersey on Saturday after returning to the United States from Paris on a private jet.
In an indictment unsealed in US District Court for the Southern District of New York, he was charged with one count of sex trafficking of minors and one count of conspiracy to commit sex trafficking of minors.
The 66-year-old pleaded not guilty.
"(Epstein) sexually exploited and abused dozens of minor girls at his homes in Manhattan, New York, and Palm Beach, Florida, among other locations," the indictment said.
Some of the victims were as young as 14.
A protest group called "Hot Mess" hold up signs of Jeffrey Epstein in front of the Federal courthouse on July 8, 2019 in New York City Source: Getty Images
Epstein, a well-connected financier whose friends have included President Donald Trump and former president Bill Clinton, was convicted previously of paying young girls for sexual massages at his Palm Beach mansion.
But Epstein avoided federal prosecution in those cases with a 2007 plea deal negotiated by his lawyers with Alexander Acosta, now the labor secretary in the Trump administration.
Under the secret deal, he pleaded guilty to a state charge of soliciting prostitution from a minor and served 13 months in a county jail.
Acosta, who was the top federal prosecutor in Miami at the time, has been the target of a campaign demanding his resignation over the relatively light sentence handed down to the billionaire financier.
