They argue the man, whose identity is unknown, has been denied constitutionally guaranteed legal rights because he remains in military custody three weeks after he was handed over to US authorities
by an allied group and has not been given access to an attorney.
"It's plain as day that the United States can't disappear an American citizen into military custody and deny him his basic rights to appear before a court with the assistance of a lawyer to challenge his detention," Jonathan Hafetz, a senior attorney for the ACLU, told CNN.
The group is arguing that the detention is unlawful and hopes to see the man transferred to a US federal court.
Last week, the ACLU sent a letter
to Secretary of Defense James Mattis and Attorney General Jeff Sessions, expressing their concerns over the case. They did not receive a response, Hafetz told CNN.
The alleged ISIS fighter's case has been shrouded in mystery since he was apprehended
by the Syrian Democratic Forces last month and turned over to the US military.
"The US citizen is being legally detained by Department of Defense personnel as a known enemy combatant," US Marine Corps Major Adrian Rankine-Galloway told CNN at the time.
At the height of the George W. Bush administration's "War on Terror," detentions of alleged "enemy combatants" were more common.
However, the administration faced several high-profile
legal challenges over the practice.
"Were (the US government) to return to the era of enemy combatant detentions, it would be a terrible decision that would undermine the United States constitution and respect for the United States throughout the world," Hafetz said.
But because there are so many unknown factors in this case, it's difficult to predict the outcome, Steve Vladeck, a CNN Supreme Court analyst and professor at the University of Texas School of Law, explained.
"It's possible that this could become a major test case not just of the government's power to subject an American citizen to military detention (which we haven't done for almost a decade), but of whether Congress has in fact authorized the use of military force (including detention) against ISIS," Vladeck told CNN in an email. "It's also possible that this gets mooted tomorrow by the detainee's transfer to foreign or criminal custody."
"But if nothing else, hopefully this suit puts pressure on the government and the courts to move toward some kind of resolution of these issues," Vladeck added.