An official with the South Korean Joint Chiefs of Staff said the North's border guards fired at least 40 rounds.
The soldier bolted from a guard post at the northern side of Panmunjom village in the Joint Security Area to the southern side of the village, according to South Korea's Joint Chiefs of Staff.
Over the decades since the peninsula was divided, dozens of North Korean soldiers have fled to the South through the DMZ, which extends for two kilometers either side of the actual borderline.
It's unclear what the soldier's conditions are or why he made a decision to defect to the South.
The defector, dressed in a combat uniform, was unarmed, Al Jazeera reported.
"Our military maintains full readiness while strengthening the alert in preparation for the possibility of provocations by the North Korean army", the JCS said. The last time a North Korean soldier defected through there was in 2007 and, before that, in 1998. An estimated 1,000 people flee Kim Jong Un's volatile regime each year, but going through the DMZ - fortified with land mines, barbed wires and machine guns - have been extremely rare because of the risky conditions.
North Korean guards immediately drew their weapons and set off in pursuit.
South Korean troops found the injured soldier south of the border after hearing sounds of gunfire, a Defence Ministry official said.
Two American soldiers also were killed in the DMZ by ax-wielding North Korean soldiers in a 1976 brawl over an attempt to trim a poplar tree. They stand only several yards away from tall South Korean soldiers wearing aviator sunglasses and standing motionless like statues.
The 1953 armistice that ended the fighting but left the countries technically at war was signed in one of the blue buildings that straddle the Military Demarcation Line. More than a million mines are believed to be buried inside the zone.
There has been speculation in both North Korea and the United States that Trump may be feigning unpredictability, emulating former USA president Richard Nixon's "Madman Theory" -whereby enemy countries were tricked into avoiding conflict with the U.S., believing Nixon would be irrational and unpredictable in his response.
North Korea has typically accused South Korea of enticing its citizens to defect, something the South denies.
Although there have been a handful of defections across the DMZ in recent years, escapes through the tense Joint Security Area are rare. That prompted Washington to send nuclear-capable B-52 bombers to intimidate the North before the adversaries pulled back from the brink of conflict.