Lindh, 38, was the first prisoner brought into a U.S. courtroom to face charges in the War on Terror, following the Sept. 11 attacks. His release comes 2 1/2 years before the completion of his 20-year sentence, which the Department of Justice's Bureau of Prisons said in a statement is attributed to Lindh's "good conduct" during his time in prison.
President Donald Trump slammed the release of Lindh on Thursday afternoon, during a White House event to announce aid for farmers affected by a trade dispute.
"Am I happy about it? Not even a little bit," Trump said.
The president told reporters that the government would be closely watching Lindh and that he checked with government lawyers to see if he could stop Lindh's release.
"I went and checked, and he said, 'From a legal standpoint there is nothing we're allowed to do, because if there was, I would have done it instantly,'" Trump said.
He added, "What bothers me more than anything else is here's a man who has not given up his proclamation of terror. And we have to let him out."
Earlier Thursday, Secretary of State Mike Pompeo blasted the convicted terrorists release after a "relatively short sentence."
"I understand he is still threatening the United States of America and still committed to the very jihad that he engaged in that killed a great American and there is something deeply troubling about that," Pomepo said in an interview on "Fox and Friends."
Lindh is expected to reside in northern Virginia, outside Washington, and is said by multiple sources to still be radicalized with extremist beliefs.
The conditions of Lindh's release include a demand that he go through mental health counseling, that he not communicate or espouse extremist views and there are several restrictions related to his internet use -- including a stipulation that he can only communicate online in English.
But Lindh's release is still not without controversy.
Sens. Richard Shelby, R-Ala., and Maggie Hassan, D-N.H., released a joint statement Tuesday expressing concern over his release and demanding more information on steps that will be taken to ensure Lindh is not a threat to public safety.
"Our highest priority is keeping America safe, secure and free," they said in the statement. "To that end, we must consider the security and safety implications for our citizens and communities who will receive individuals like John Walker Lindh who continue to openly call for extremist violence."
Shelby had previously said in April that President Donald Trump had told him he opposed Lindh not serving his full sentence, but it's unclear whether Trump plans to weigh in publicly on the matter. The Department of Justice public affairs office did not respond to a request for comment.
Lindh stayed in Osama bin Laden's guest house -- eventually meeting and "thanking" the leader of the terrorist organization, court documents said.
He trained with 20 other Taliban fighters at a camp in Afghanistan on "weapons, orienteering, navigation, explosives and battlefield combat, which included the use of shoulder weapons, pistols, and rocket-propelled grenades, and the construction of Molotov cocktails," court documents said.
According to court documents, Lindh "swore allegiance to jihad," and stayed with the Taliban despite knowing that bin Laden carried out the attacks on Sept. 11.
He was captured by Northern Alliance fighters after the U.S. invasion of Afghanistan in 2001.
CIA paramilitary officer Johnny "Mike" Spann, 34, was killed in a Taliban prisoner uprising, shortly after questioning the captured Lindh. He was initially charged with conspiracy in Spann's murder, but those charges were dropped as part of an eventual plea bargain.
Spann's father, Johnny Spann, told ABC News in an interview on Sunday that he objects to Lindh getting out three years early for good behavior.
ABC's James Meek contributed reporting to this piece.