The soldier crossed to the South Korean side of the Joint Security Area (JSA) in the village of Panmunjom on Monday.
He had driven near the JSA, but had to finish his journey by foot when a wheel came loose, the South said.
North Korean troops shot at him 40 times - but he made it across and was found under a pile of leaves, it added.
About 1,000 people from the North flee to the South each year - but very few defect via the Demilitarised Zone (DMZ), which is one of the world's most heavily guarded strips of land.
It is even more unusual for North Koreans to cross at the JSA, which is a tourist attraction, and the only portion of the DMZ where both forces stand face-to-face.
North and South Korea are technically still at war, since the conflict between them ended in 1953 with a truce and not a formal peace treaty.