In one of his first acts after taking office last month, Obama ordered US government lawyers to review al-Marri's case.
He was later transferred to a jail in Illinois where he was charged with conspiracy and providing material support to terrorism.
Al-Marri was arrested in late 2001 as part of the US Federal Bureau of Investigation's probe into the September 11 attacks.
Prosecutors initially indicted him on charges of credit card fraud and lying to the FBI, although al-Marri also denied those charges.
In June 2003, Bush said al-Marri had vital information about potential attacks, declared him an enemy combatant and ordered him transferred to military custody.