The 'low-ranking' officer crossed the border in thick fog
South Korean guards have fired about 20 warning shots at North Korean troops searching for a defector.
The soldier fled across the heavily guarded demilitarised zone that divides the two countries, South Korea's Yonhap news agency said.
The "low-ranking" officer was seen by South Korean soldiers using surveillance equipment as he crossed the border in thick fog and made his way to a guard post, a ministry spokesman said.
Although no shots were fired at the time, South Korean troops later fired 20 rounds using a K-3 machine gun to warn off North Korean guards who approached the border looking for the man.
The spokesman for South Korea's joint chief of staff, Roh Jae-cheon, said: "Today a North Korean soldier defected through our military's general outpost in the centre-western region.
"Our military secured his safety, and a questioning will be conducted by related agencies to find out the background of his defection and motive."
It comes after the defection of another North Korean soldier at the truce village of Panmunjom, where opposing forces watch each other across a concrete dividing line.
He was shot at least four times by his own comrades, who used handguns and automatic rifles to fire about 40 rounds at him.
Pyongyang has been accused of violating the 1953 armistice agreement between the North and South by firing across the line dividing the two countries last month.
Soldiers on the South did not return fire.
The defector, 24-year-old Oh Chong-Song, is recovering in hospital after being pulled to safety by two South Korean soldiers.
Thursday's defection is the fourth by a soldier crossing the demilitarised zone this year.
About 30,000 North Koreans have defected to South Korea, mostly via China, since the end of the 1950-53 Korean War.
Tensions between the two countries are high and have been inflamed by North Korea accelerating its weapons tests as part of its goal of achieving a nuclear missile capable of striking anywhere in the United States.
Last month, North Korea test-fired its biggest and most powerful intercontinental ballistic missile.