According to the South’s Joint Chiefs of Staff (JSC), the man was spotted on thermal imaging equipment as he made his way to the border between the two Koreas on Wednesday night.
He was picked up near the Imjin river, which flows from the North to the South across the DMZ, and placed in military custody.
The JSC said he wanted to defect when they apprehended him.
The apparent defection came as it emerged that a North Korean diplomat who went into hiding in Italy last year was under protection outside the country, according to South Korea's spy agency.
Legislator Lee Eun-jae said National Intelligence Service officials told a closed-door briefing that Jo Song Gil, North Korea's former acting ambassador in Rome, has left Italy and is being protected “somewhere".
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Ms Lee said the spy agency apparently meant a third country but did not reveal which one.
The NIS officials did not provide a specific answer when asked whether South Korea was involved in protecting Mr Jo, she said.
The NIS told legislators in January that Mr Jo went into hiding with his wife in November, but the agency has a mixed record on tracking developments among North Korea's ruling elite, which is made difficult by Pyongyang's stringent control of information.
North Korea, which is extremely sensitive about high-profile defections, has yet to publicly comment on Mr Jo's situation, according to Seoul's Unification Ministry.
Some experts believe the North may continue to ignore the apparent defection to avoid highlighting the vulnerabilities of its government while it engages in negotiations with Washington to leverage its nuclear arsenal for economic and security benefits.