The T-50B aircraft manned by a 32-year-old flight lieutenant hit the side of the mountain in the northeastern county of Hoengseong during a training flight for an air show, a ministry spokesman said.
"The pilot was found dead near the crash site," he said, adding an investigation was underway into the cause of the accident.
The crash sparked a brush fire which was quickly extinguished by firefighters, Yonhap news agency said.
Some witnesses had reported seeing a parachute, which originally led rescuers to believe the pilot might have survived.
Military officials said it was the first-ever crash involving a T-50B, which is a variant of South Korea's first home-made supersonic aircraft, the T-50, and is used by the air force's Black Eagle air show team.
Since its maiden flight in 2002, the T-50 has been produced in aerobatic and combat variants, including the TA-50 light attack aircraft which South Korea has been actively pushing for export.
Indonesia has ordered 16 TA-50 light fighters, and South Korea is pursuing other contracts from the Philippines, the United Arab Emirates and Iraq.