The Centers for Disease Control & Prevention said the 43-year-old was diagnosed on Tuesday and was being treated in Gwangju city.
Zika, a mosquito-borne virus, has been declared a global health emergency by the World Health Organization.
It has spread rapidly in Brazil and the Americas, and is suspected of causing birth defects.
But WHO experts caution the link between the virus and microcephaly - in which babies are born with underdeveloped heads - is not yet proven.
Isolated Zika infections have been reported in a handful of countries in Asia.
South Korea said the infected man had been quarantined and his movements tracked since returning home, according to the Yonhap news agency.
- BBC
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