The 60-year-old made the dangerous journey into the hermit kingdom but was returned home via the border village of Panmunjom – a site commonly used to host high-level diplomatic talks between the two nations.
North Korea says the man had “illegally entered” the country last month.
South Korea’s Unification Ministry said officials are investigating how and why the man made the perilous journey but thanked Pyongyang for returning him from “from a humanitarian standpoint”.
North Korea is accused of abducting nearly 4,000 foreign citizens since the Korean War ended in 1953 with the majority of victims coming from Japan or South Korea.
Pyongyang has repatriated citizens from the South in the past in the hope Seoul will respond in kind and deliver North Korean defectors back to the hermit kingdom.
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But this latest gesture is just the second time the North has returned a South Korean citizen back across the border since November 2011, the Singapore-based Straits Times reports.
The repatriation by Kim’s regime this week comes amid a recent thawing in relations comes as the two Koreas met for peace talks.
North and South Korea are still technically at war after a three-year conflict from 1950 to 1953 ended with a truce but not a peace treaty.
Diplomats from Seoul and Pyongyang held their first ever three-way talks with the United Nations Command (UNC) at Panmunjom yesterday (Tuesday) to discuss ways to demilitarise the border.
The 160-mile long frontier was imposed after the Korean War and separates North from South with miles of barbed wire fences, heavily fortified bunkers and huge minefields.
The talks involved reducing the amount of weaponry and troops deployed on the border, removing guard posts and adjusting surveillance equipment, South Korea’s defence ministry said.
The two Koreas had already agreed this week to begin reconnecting rail and road links.
But the United States has warned the improvement in relations could serve to undermine efforts to force Kim Jong-un to surrender his nuclear weapons.
President Donald Trump met face-to-face with the North Korean dictator at a summit in June with the aim of paving the way for the denuclearisation of the Korean Peninsula.
The meeting was declared a success by Mr Trump who said he had agreed to provide “security guarantees” to North Korea in exchange for a further commitment from Kim to work towards nuclear disarmament.
But in August, just two months after the historic summit, Mr Trump’s national security adviser John Bolton revealed the hermit kingdom had “not taken the steps we feel are necessary to denuclearise”.
And in September, North Korean state media renewed its aggressive rhetoric against the US and the Trump administration after a period of relative silence.
An editorial in the regime-run Rodong Sinmun newspaper warned the US of negative consequences if it attempts to scupper improvements in relations between North and South Korea.