The Pentagon said Younis Abdurrahman Chekkouri was sent home to Morocco following a "comprehensive" security review that saw six US departments and agencies unanimously approve him for transfer.
He was transferred on Wednesday, said a Pentagon official, who did not say whether Chekkouri would be imprisoned, placed under house arrest or released.
The 47-year-old was captured by Pakistani forces in late December 2001 with a group of several dozen Arab fighters who had fled the Tora Bora cave complex in eastern Afghanistan, a stronghold of the Taliban and its Al-Qaeda allies.
Following his release, 115 detainees still remain in the prison opened to hold terror suspects following the September 11 attacks in 2001.
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That's less than half the number who were detained there (242) when President Barack Obama took office in January 2009.
Obama has vowed to close the prison but has struggled to do so in the face of domestic opposition at home in Congress and abroad from allies reluctant to take in one-time terror suspects.
He now has just a little more than a year to fulfill his promise.