The top court refused to take up a petition on behalf of Moath al-Alwi, who was arrested on the Afghan-Pakistan border in December 2001 and transferred to Guantanamo the following January.
The Yemeni national, who was born in 1977, is suspected of having been a body guard of al-Qaeda leader Osama bin Laden, which he denies. He is considered to be an "enemy combatant," a classification that allows him to be held for the duration of the conflict.
Alwi's lawyers argued that unlike past conflicts, the war in Afghanistan and against al-Qaeda is of indefinite duration, creating "the risk of lifelong detention for him."
Their arguments did not persuade the court, which gave no reason for rejecting the case.
Justice Stephen Breyer, a liberal, wrote a dissent regretting his colleagues decision.
"In my judgement, it is past time to confront the difficult question," he wrote.
Breyer noted that a court of appeals had ruled in favour of the government's argument that Alwi could be held as long a state of armed hostilities persist.
But he said, the government "does not state that any end is in sight."
"As a consequence, al-Alwi faces the real prospect that he will spend the rest of his life in detention based on his status as an enemy combatant a generation ago, even though today's conflict may differ substantially from the one Congress anticipated" when it authorized the use of force.
The prison at Guantanamo was opened in 2001 on a US naval base on the southeastern tip of Cuba to hold the al-Qaeda and Taliban fighters captured in Afghanistan following the September 11, 2001 attacks on the US.
Of the 780 prisoners held there, only about 40 remain. No new prisoners have been transferred there since 2008, although US President Donald Trump signed an order in January 2018 keeping the prison open.
