The soldier was found on the southern side of the border village of Panmunjom, about 50 meters south of the military demarcation line.
He was wounded in a shoulder and an elbow after being shot by one of his erstwhile comrades while making a dash from a nearby North Korean guard post.
A South Korean Defense Ministry said "there was no exchange of fire with our side."
But since the defector had fallen in an area that could be exposed to the North Korea fire, he added, "we had to crawl there to get him out."
Once the North Korean had been recovered he was transferred to a hospital at Suwon, south of Seoul, in a helicopter of the United Nations Command.
The soldier's condition and his rank remained under wraps last night.
On average, more than 1,000 North Koreans defect to South Korea every year, but most travel via China while some flee by boat.
Indeed, it is unusual for a North Korean to cross the land border dividing the Koreas, which have been in a technical state of war since their 1950-53 conflict ended in a truce rather than a peace treaty. The last such crossing was in June.
The defection came amid heightened tension between the Koreas and between the United States and the North.
North Korea has this year been boosting its nuclear and missile capacity with a series of tests as it attempts to face down the US administration, while President Donald Trump vows he will prevent it from being able to hit the US mainland with a nuclear weapon.
North Korea conducted its sixth and most powerful nuclear bomb test on September 3 but has not launched any missiles since firing one over Japan on September 15 - the longest lull this year.