Maalik Alim Jones, 31, "was charged with providing material support to al Shabaab and receiving training from the terrorist organization," Assistant Attorney General for National Security John Carlin said in a statement released by the department.
Prosecutors said the suspect traveled to Somalia, received military training from al Shabaab, and took up arms as a terrorist fighter with an organization that has declared the United States a target.
"Having allegedly sworn allegiance to al Shabaab, a terrorist organization bent on destroying America, Maalik Jones will now face American justice in a Manhattan federal court," Manhattan US Attorney Preet Bharara said in a statement.
A lawyer for Jones was not listed in online court documents.
Jones has appeared with other al Shabaab fighters in at least two videos that were recovered from an al Shabaab fighter, prosecutors said.
In one, he possessed a firearm, and is seen with several al Shabaab fighters who participated in a June 2015 attack on a Kenyan Defense Force base where two Kenyan soldiers were killed, they said in a statement.
The case comes just days after two men from the Middle East who came to the United States as refugees were arrested on federal terrorism charges in California and Texas last week for supporting Islamic militant groups.
There have been more than 75 publicized arrests of US residents who have allegedly become radicalized by Muslim militants since 2014.