The teenager approached a South Korean guard post in north-eastern Hwacheon in the demilitarised zone (DMZ) on Monday, South Korea's defence ministry said.
There was no exchange of fire and the soldier is now being held in custody.
It is extremely rare for defectors to walk across the DMZ. The last time it happened was in 2012.
Most defectors cross over into China, then make their way through South East Asia and then into South Korea.
Of the nearly 28,000 North Koreans who have resettled in the South, most of them left the country through the border with China, and not through the DMZ.
This is because the 250km-(155 mile)-long demilitarized zone is heavily guarded, littered with anti-personnel landmines.
The last time a North Korean soldier defected through the wire fence was in October 2012, when a soldier managed to cross undetected.
This was a huge embarrassment for the South Korean military and steps were taken to strengthen border security.
Recently, there has been increased activity by North Korean soldiers in the DMZ and some believe the North has been trying to make defections more difficult.
The DMZ is fortified with landmines and barbed wire and guarded by tens of thousands of troops on both side.
Hundreds of North Koreans flee poverty and a repressive regime at home each year.
In August last year, two North Koreans swam across the Yellow Sea border to a South Korean island.
A North Korean soldier has walked across one of the world's most heavily militarised borders to defect to the South, officials say.