The man crossed the military demarcation line around 01:00 GMT on the central-eastern part of the border, Seoul's Joint Chiefs of Staff (JCS) said.
There was no exchange of fire during the defection.
"He is now being held in custody for questioning", the JCS added.
It is rare for North Korean defectors to walk across the mine-riddled border, which is guarded by tens of thousands of soldiers on both sides.
The last time in happened was June last year when a teenage North Korean soldier surrendered himself to South Korean border guards at Hwacheon, north-east of Seoul.
Most cross the porous frontier with China first before travelling through a south-east Asian nation and eventually arriving in South Korea.
In 2012, a North Korean soldier walked unchecked through rows of electrified fencing and surveillance cameras, prompting Seoul to sack three field commanders for a security lapse.
In August 2014, two North Koreans swam across the Yellow sea border to a South Korean frontline island.
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