Liban Haji Mohamed was arrested as he traveled from an area controlled by terror group Al-Shabaab in southern Somalia.
The one-time cabdriver in northern Virginia is being held and interrogated by Somali officials.
Somalia’s National Intelligence and Security Agency did not say when Mohamed was captured but said the suspect had been under surveillance for several days.
Mohamed was born in Somalia but is a naturalized U.S. citizen.
The 29-year-old left the United States in July 2012 to join al Qaeda in Somalia, according to CNN affiliate WTKR-TV, citing the FBI.
Mohamed is wanted by the FBI for allegedly providing material support to terrorists, but his extradition is not assured, as the United States and Somalia do not have an extradition treaty in place.