Thae Yong Ho, minister at the North Korean embassy in London, has arrived in South Korea with his family, Seoul’s unification ministry said.
Mr Thae told South Korean officials that he decided to defect because of his disgust with the government of North Korean leader Kim Jong Un, his yearning for South Korean democracy and worries about the future of his children, said ministry spokesman Jeong Joon-Hee.
Mr Jeong said Mr Thae was the second highest official in North Korea’s embassy, and is the most senior North Korean diplomat to defect to South Korea.
In 1997, the North Korean ambassador to Egypt fled but resettled in the US.
The highest level North Korean to seek asylum in South Korea is Hwang Jang-yop, a senior ruling Workers’ Party official who once tutored Kim Jong Un’s late father dictator Kim Jong Il.
Mr Hwang’s 1997 defection was hailed by many South Koreans as an intelligence bonanza and a sign that the North’s political system was inferior to the South’s. Mr Hwang died in 2010.
Defections are a source of bitter contention between the rival Koreas, and South Korea does not always make high-profile cases public.
North Korea often accuses the South of kidnapping or enticing its citizens to defect.