Ulbricht was convicted of conspiracy to commit drug trafficking, money laundering and computer hacking.
During the trial, prosecutors said that Ulbricht’s website, hosted on the hidden “dark web”, anonymously sold more than $200 million (£131 million) worth of drugs.
He ran Silk Road under the alias Dread Pirate Roberts, a reference to the character in the 1987 film The Princess Bride.
Prosecutors said he also instigated six murders for hire, including the killing of a former Silk Road employee, although they said there was no evidence that any murders were actually committed.
The Silk Road got its name from the historical trade routes that spanned Europe, Asia and parts of Africa.
The site gained notoriety through media reports and online chatter. But users could only access the site through Tor, a system that allows people to use the network without revealing who they are or what country they are in.
FBI court documents said the site had just under a million registered users, but investigators said they did not know how many were active.
Verdict to Ulbricht – who has two university degrees – District Judge Catherine Forrest said he was “no better person than any other drug dealer”.
She said the site was his “carefully planned life’s work”.
The judge noted that the long sentence also served as a signal to the captains that there would be “very serious consequences.”
“I wanted to empower people to make choices in their lives and to have privacy and anonymity,” Ulbricht said during his sentencing in May 2015.
Trump previously hinted that he planned to commute Ulbricht’s sentence during a speech at the Libertarian National Convention last year.
The Libertarian Party advocated for Ulbricht’s release and said his case was an example of government overreach.
Republican Congressman Thomas Massey, a Trump ally, applauded the president’s decision.
“Thank you for keeping your word to me and others who advocated for Ross’s freedom,” said the Kentucky lawmaker.