The soldier was shot in the shoulder and elbow and was picked up bleeding on the South side of a portion of the border known as the Joint Security Area.
It is rare for the North's troops to defect at the truce village, a major tourist attraction and the only part of the frontier where forces from the two sides come face-to-face.
"Our military has taken in a North Korean soldier after he crossed from a North Korea post towards our Freedom House," Seoul's Joint Chiefs of Staff (JCS) said in a statement, referring to a building on the South side of the village which is bisected by the borderline.
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An JCS official quoted by Yonhap news agency said the soldier was evacuated to a private hospital by a UN helicopter.
The official said the South's soldiers heard a gunshot and then retrieved the unarmed and bleeding soldier in the mid-afternoon.
No personal details have been released but his uniform suggested he was low-ranking, Yonhap said.
The JCS official said the soldier had regained consciousness but declined comment on whether his injuries were life-threatening.
There has been no exchange of gunfire between the two sides, but the South's military said it has raised its level of alertness against any North Korean provocations.
No tourists were in the Joint Security Area at the time because such tours do not run on Monday, said a spokesperson for United States Forces Korea which approves the visits.
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Military officials from the two sides have used Panmunjom frequently in the past for talks. Unlike the rest of the frontier, Panmunjom is not fortified and the border is marked only by a low concrete divider.
Over the decades since the peninsula was divided, dozens of North Korean soldiers have fled to the South through the heavily fortified Demilitarised Zone (DMZ) along the rest of the border.
Two North Korean soldiers came over to the South in June after crossing the frontier.
Relations between the two sides have been tense for months, as the North stepped up its missile tests. In September it carried out its sixth and largest nuclear test, of what it described as a hydrogen bomb.
More than 30,000 North Korean civilians have fled their homeland since the two nations came into being in 1948. But it is very rare for civilians to cross the closely guarded border with the South, which is fortified with minefields and barbed wire.
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