The soldier crossed to South Korea from the North Korean side of the heavily guarded Joint Security Area (JSA) to Freedom House in the South, according to the JCS.
The man who is reportedly a low ranking soldier, was shot in the shoulder and elbow and was picked up bleeding on the south side of the border known as the Joint Security Area (JSA).
South Korean troops found the injured soldier south of the border after hearing sounds of gunfire, a Defence Ministry official said.
"In the afternoon today, a North Korean soldier defected from a guard post on the North Korean side of the JSA toward our side and our military took him", the Yonhap news agency quoted an unidentified military official as saying. He was unconscious and in critical condition on Tuesday, the surgeon in charge of the soldier's treatment, Lee Cook-jong, told reporters.
North Korea has typically accused South Korea of enticing its citizens to defect, something the South denies.
It wasn't immediately known how serious the soldier's injuries were or why he made a decision to defect.
"His organs are extremely damaged. we do not know how long he can hold up", Lee said, describing the soldier's condition as "very serious".
Col. Roh Jae-cheon, a spokesman for South Korea's Joint Chiefs of Staff, said the military first became aware of the situation around 3:31 p.m.
All channels for dialogue are now cut off between Seoul and Pyongyang after North Korea's relentless development of nuclear weapons and missiles. What were they really doing when the defector received multiple gunshots from North Korean guards?
He was shot by a North Korean soldier but succeeded in crossing, the JCS added, and has been evacuated for medical treatment. South Korean troops didn't fire at the North, he said.
The area is a popular place for tourists and visiting officials, not least because once inside the blue meeting huts that straddle the border, visitors can technically cross the line, although soldiers guard the doors out to the other side.
Areas around Panmunjom were the site of bloodshed and defection attempts by North Koreans in the past, but there have been no such incidents in recent years. That prompted Washington to send nuclear-capable B-52 bombers to intimidate the North before the adversaries pulled back from the brink of conflict.