Mohamed Ibrahim Ahmed, who is a citizen of Eritrea, is accused of receiving weapons and explosives training from al-Shabab. The militant group is seeking to further destabilize Somalia's weak transitional government and is considered a terrorist organization by the United States. Ahmed is also charged with providing financial support to al-Shabab.
Ahmed is to appear in federal court again on Tuesday where he is expected to plead not guilty to the charges.
Islamist insurgent groups like al-Shabab control most of Somalia's center and south.
An African man arrested in Nigeria and brought to the United States on Saturday has been charged in New York with aiding an al-Qaida-linked terrorist organization in Somalia.