Choe In-guk is the son of two high level diplomats who also defected to the North in the 1980s.
According to North Korean state media he will live in the North and work on reunification issues.
Defections this way are very rare. It is more common for people from the North to try to escape to the South.
The two countries are technically still at war and South Koreans need permission to visit the North.
"It's not yet clear how exactly his defection came about," Oliver Hotham of specialist news site NK News, based in Seoul, told the BBC.
"But it would be fairly simple for a South Korean to get to the North if they had the regime's blessing by travelling through China."
But if Mr Choe has violated South Korean law by not seeking permission, he could potentially be arrested if he ever returned to the South, experts say.
More about: NorthKorea