US District Judge Katherine Forrest in Manhattan scheduled the trial for Nov. 3 as Ross Ulbricht, 29, pleaded not guilty to a four-count indictment unveiled on Tuesday. The charges include money laundering conspiracy and engaging in a continuing criminal enterprise.
"I know your client is in custody, so I'm sure you'd like to get this done sooner rather than later," Forrest said to Ulbricht's lawyer on Friday.
Ulbricht, who prosecutors say went online by the name "Dread Pirate Roberts", has been incarcerated since his arrest in October.
Prosecutors say that Ulbricht owned and operated Silk Road, which they allege sold drugs and criminal services in exchange for the digital currency bitcoin.
The bulk of the items for sale on Silk Road were illegal drugs including heroin, cocaine and ecstasy, prosecutors say. The site also carried listings for computer hacking services, forgeries and malicious software, according to authorities.
Prosecutors say that Ulbricht, managing a small staff of paid site administrators, reaped tens of millions of dollars in commissions through Silk Road.
The indictment charges Ulbricht with one count each of narcotics conspiracy, engaging in a continuing criminal enterprise, conspiracy to commit computer hacking and money laundering conspiracy.
US authorities have to date seized 173,991 bitcoins that at current exchange rates are worth more than $130 million, according to CoinDesk, a bitcoin price index publisher.
Federal authorities have separately charged three men -Andrew Jones, Gary Davis and Peter Nash - in connection with their alleged roles in assisting Ulbricht in operating Silk Road.
The case is US v. Ulbricht, US District Court, Southern District of New York, No. 13-06919.