Prosecutors in the port city of Incheon said the driver, Yang Hoe-jung, turned himself in at their office.
Pyongyang said it would put two US tourists on trial for committing crimes against the state.
Two months after the Sewol ferry sank, the surviving children were brought to school under a police escort.
Most of the bodies found were from children frantically trying to climb the walls or floors to escape.
The US said it was watching the Korean peninsula after reports that North Korea may be planning nuclear tests.
Relatives have criticised the slow response of government and contradictory information given by authorities.