The 19-year-old injured five more soldiers and fled from an outpost near the border with North Korea, officials say.
The army private opened fire on fellow soldiers on Saturday evening at a post in the eastern Gangwon province.
It is not yet clear what motivated him to kill his colleagues. A man hunt is now under way.
Tensions between North Korea and South Korea have been high, but there is no sign this was a cross-border incident.
“He shot dead five fellow soldiers, wounded five others and then fled the scene with his rifle and ammunition,” an army spokesman was quoted by news agency AFP as saying.
The shooting took place at an army unit near the border town of Goseong, according to South Korean news agency, Yonhap.
Tens of thousands of soldiers from both North Korea and South Korea are stationed along their joint border, one of the most heavily fortified in the world.
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