Police said on Friday that he was among a group of men who caught five amphibians at a reservoir near the city of Daejeon in March.
Believing the animals were bullfrogs, the men cooked and ate them at a restaurant days later.
The 57-year-old man began vomiting soon after and was rushed to a hospital, where he died the next morning.
Police said bufotenin, a chemical commonly found in toad toxin, was found in the leftovers of the meal.
They said that among the five animals they had caught, some were in fact toads which looked identical to bullfrogs, reported Yonhap news agency.
The man's friends showed similar poisoning symptoms but survived.
The BBC's South Korea correspondent Stephen Evans says bullfrogs are a delicacy in some parts of rural South Korea.
Some species of toads secrete venom through their skin when agitated or when they sense they are in danger.
Bufotenin can be fatal when ingested in large amounts. But it is also a natural psychedelic, giving rise to a sub culture where some lick toads in an attempt to achieve a hallucinogenic high.