"The KDCA confirmed the infection with the Naegleria fowleri ameba in a deceased patient with brain meningitis, who has recently returned from abroad," the agency tweeted.
The patient was in Thailand for four months before returning to South Korea on December 10, where he died on December 21 after experiencing headache, fever, vomiting, speech dysfunction and other symptoms.
The disease control agency will investigate the exact route of infection.
The main infection pathway is through a human's contact with contaminated water. The Naegleria fowleri amoeba can cause a rare brain infection called primary amebic meningoencephalitis and is usually fatal.