The soldier, aged in his late teens or early 20s, was carrying a personal firearm when he crossed the DMZ in heavy fog just after 8.00 a.m. local time, South Korean authorities said.
It is the second defection across the heavily-guarded border in less than two months; another North Korean soldier was shot multiple times while dramatically escaping to the South on November 13.
No shots were fired during the latest defection, South Korea's Joint Chiefs of Staff said. However, more than one hour later, around 9.30 a.m., South Korean soldiers fired 20 warning shots as North Korean soldiers appeared to search for the defector.
Several other gunshots were heard from the northern side of the border at 10.13 a.m. and 10.16 a.m., South Korean authorities said.
The defector is in custody and is likely being questioned as authorities investigate the reasons behind his defection, and seek other information about his life in one of the world's most reclusive states.
Another North Korean soldier who defected to the South spoke to CNN in November about the harsh conditions endured by military servicemen in North Korea.
Kang Ri Hyuk said soldiers in his home country were dying of hunger and disease.
"There are countless soldiers in North Korea who cannot even walk because of malnourishment," he told CNN. "The UN is sending rice and fertilizer to North Korea, but not a single grain goes to North Korea's ordinary people."
Fourth defection in 2017
Prior to this year, there had only been four defections from North Korea's armed forces in the past five years: one in 2016, one in 2015 and two in 2012.
John Delury, associate professor at the Yonsei University Graduate School of International Studies in Seoul, told CNN it was far to early to draw any conclusions from the numbers of defections in 2017.
"There are often individual motives to spur this ... four in a year is not enough to constitute evidence of something systemic," he said. "There would be need to be a lot more (defections) I would say."
The most high profile was in November when a North Korean defector, named Oh Chong Song, was shot multiple times after driving to the border in a jeep.
While attempting to pursue Oh, North Korean soldiers fired across the demilitarized zone, violating the Korean War armistice
Following Oh's desertion, fellow deserter Kang told CNN the soldier's flight would give hope to other military members hoping to flee.
"This incident was an opportunity to give courage to other North Korean soldiers serving in the military in the DMZ," he said in November. "I think we could see another soldier crossing the border with a jeep."
The North Korean military has more than 1.2 million active soldiers and a further 7.7 million in reserves. It is one of the largest ground forces in the world.