INTERNATIONAL NEWS - The North Korean soldier had walked across the Demilitarised Zone (DMZ) shortly after 08:00 (23:00 GMT Wednesday).
He had emerged from thick fog at a checkpoint, said the South's military.
He is the fourth North Korean soldier to defect this year. The incident comes weeks after one of the most dramatic defections in recent times.
In that incident, on 13 November, a soldier was shot as he fled across to the southern side of the Joint Security Area (JSA) in the village of Panmunjom.
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Thursday's incident took place at a checkpoint in the mid-western frontline, said Roh Jae-cheon, spokesman for South Korea's joint chiefs of staff.
Heavy fog had descended on the area, limiting visibility to about 100m (110 yards), he told reporters. But as the North Korean soldier approached the post, his movements were picked up on surveillance equipment.
Mr Roh added that the defector was taken into custody and was "safely secured". Authorities are now investigating what drove him to make the crossing.
The soldier, thought to be 19 years old, was carrying an AK-47 rifle, reported The Korea Herald citing the military. No gunfire was exchanged at the time.
But shortly after his crossing, a group of border guards from the North approached the border, appearing to search for their comrade, according to South Korea's defence ministry. South Korean soldiers fired about 20 warning shots.
