Eric Harroun is in federal custody in the United States charged with conspiracy to use a weapon of mass destruction outside the US.
Court documents allege Harroun was working side-by-side with the al Nusra Front, branded by the US a terrorist organisation.
In March, Harroun went to the US consulate in Istanbul, and agreed to be interviewed by the FBI.
He told officials he joined the Free Syrian Army and was picked up by the al Nusra Front. According to Harroun, he was treated as a prisoner for a while, but then fought alongside them to help overthrow Syrian leader al-Assad.
While the US also wants to overthrow Assad, legal experts say that does not play into the US government's decision to charge him.
Al Jazeera's John Terrett reports from Washington DC.