A search operation was underway after the person was detected at about 9.20pm local time on Saturday on the eastern side of the demilitarised zone separating the two countries, the Joint Chiefs of Staff (JCS) said.
"We have confirmed that the person crossed the military demarcation line border at about 10.40pm and defected to the North," the JCS said.
The JCS said while it could not confirm whether the person was alive, it had sent a notice to the North via a military hotline asking for protection.
Crossing the border is illegal in South Korea and came as North Korea carries out strict anti-coronavirus measures since shutting borders in early 2020, although it has not confirmed any infections.
There was a public and political uproar after North Korean troops shot dead a South Korean fisheries official, who had gone missing at sea in September 2020, for which Pyongyang blamed anti-virus rules and apologised.
Two months earlier, North Korean leader Kim Jong-un declared a national emergency and sealed off the border after a North Korean defector who reportedly had Covid-19 symptoms illegally crossed the border into the North from the South.
The North's prolonged lockdowns and restrictions on inter-provincial movement have pushed the number of North Korean defectors arriving in the South to a record low.
Kim Jong-un - in pictures
Cross-border relations soured after denuclearisation negotiations between Pyongyang and Washington stalled after a failed summit in 2019.
South Korea and a US-led UN force are technically still at war with North Korea as the 1950-53 Korean War ended in an armistice rather than a peace treaty.