The soldier crossed the frontier through the Korean Demilitarised Zone (DMZ) on foot and unarmed, a spokesperson from the Defence Ministry told EFE news.
He added South Korea has opened an investigation to find out details of the defection, including what led to it.
The South's armed forces posted near the border have also raised their alert owing to the possibility of a "provocation" from the North's army in retaliation to the defection, he stated.
The DMZ, a strip of land with tight security on both sides, is a rare choice of place to flee from North Korea to South Korea, and only 60 dissidents, including both civilians and military personnel, from the Kim Jong-un-led country have managed to make the crossover since 2010.
The last North Korean soldier to have made the passage through the DMZ was in June last year, in a week-long journey through the forest in order to escape the beatings he received in the North's Army.
In the last few years, between 1,000 to 3,000 North Koreans, including soldiers, have crossed over to the South but mostly through North Korea's northern border with China.
