The Korea Disease Control and Prevention Agency says the patient, who was in his 50s, had entered South Korea on Dec 10, after a four-month stay in Thailand.
He had begun suffering from headaches, fever, vomiting, slurred speech and stiffness of the neck on the evening of his arrival, and had been sent to a hospital the next day. He was pronounced dead on Dec 21.
This is the first official case of a Naegleria fowleri infection in South Korea. The first ever infection was reported in the US state of Virginia in 1937.
The amoeba is said to enter the body through inhalation from the nose, where it then travels to the brain.
The KDCA has advised residents to refrain from swimming in regions and neighbourhoods where the disease broke out.
It says most infections happen through swimming, but notes that the risk of infection is not high.
“To prevent infection, we recommend avoiding swimming and leisure-related activities and using clean water when travelling to areas where cases have been reported,” it says.
381 cases have been reported around the globe as of 2018, including in India, Thailand and China.