Seoul's unification ministry announced that the 52-year-old man surnamed Ma was returned to the South on Friday through the western truce village of Panmunjom.
National news agency Yonhap quoted Park Soo-jin, the ministry's deputy spokesperson, as saying, "The government will proceed with medical check-ups for him and work to confirm the reason for, and method of, his entry into the North."
According to North Korea, Ma entered the country illegally in late November.
While tens of thousands of North Koreans have fled to the South after the 1950-53 Korean War, defections to the North seldom happen.
Despite Pyongyang typically permitting defectors to remain in the reclusive state, in a recent case in September, the North returned a South Korean man who had entered the country through China.
Last year, Pyongyang repatriated six South Koreans who crossed the border from 2009 to 2012.
The Koreas technically remain at war after an armistice, rather than a peace treaty, brought the Korean War to a close.