Jose Darwin Flores, 32, of Arlington, is being held without bond on a kidnapping charge, but Warren County Sheriff Johnny Williams said he will face other charges once police complete their investigation.
The hijacking happened while the bus was heading south on Interstate 85 late Thursday, Williams said.
"He just stood up with a gun and took control of the bus," Williams said.
The driver pulled off the highway about 60 miles north of Raleigh and let off all the passengers except two.
Police received word of a hijacking and started to follow the bus before it stopped. Flores was arrested after being zapped with a stun gun.
Flores does not yet have a lawyer and investigators have been unable to determine a possible motive, Williams said.
"We haven't been able to get that far with him yet," he said.
The bus trip began in Richmond, Va. and was headed to Raleigh. Passengers were eventually put on another bus and taken to their destinations.
Flores has a criminal record that includes a drunken driving conviction in 2007 in Alexandria, Va. He was sentenced to 20 days in jail. In August, he was arrested for being drunk in public, said Arlington Police spokeswoman Crystal Nosal, who declined to release any details. Flores was convicted in October and ordered to pay $131 in fines.
Flores' mother said Friday she didn't have any additional details on her son's arrest.
"What's there to say? My son is sick," Maria Flores said in Spanish over the phone from her Virginia home. She didn't elaborate and hung up.