The jet crashed into a mountain in Hwaseong, about 50 kilometres south of the capital Seoul, according to military authorities.
The single pilot on board failed to eject and was killed in the crash, the defence ministry said in a statement.
The airforce said it was investigating the cause of the accident.
The F-5E is an older generation fighter jet with a design that dates back to the 1960s.
Last week, South Korea grounded its entire fleet of advanced F-35 fighter jets, after one of them was forced to make a dramatic emergency landing after a major systems malfunction.
After the landing gear on the jet stopped working, the pilot chose not to eject and instead landed the jet on its belly -- walking away without any injuries.
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