Muhanad Mahmoud al-Farekh was deported from Pakistan, where he had travelled to in about 2007.
He and two others travelled to the Federally Administered Tribal Areas of Pakistan from Winnipeg, Canada, where they were students.
Mr al-Farekh was born in Texas, and has been charged in New York.
He is accused of supporting a conspiracy to kill Americans and to carry out attacks against the US military.
A statement from the US Department of Justice and court documents say that Mr al-Farekh, a man named Ferid Imam, and one other unnamed individual allegedly left Canada, where they were students at the University of Manitoba, to travel to Pakistan and fight against American forces.
The justice department says that the trio did not discuss their plans with associates before leaving.
However, one of the men called a friend to tell him that he should not expect to see him again because he wished to become a martyr.
The US Justice Department says it has charged an American citizen with conspiracy to provide material support to al-Qaeda militants in Pakistan.