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Mycotoxin contamination of food grains is a food safety hazard, and zearalenone (ZEN) is one such mycotoxin affecting rice grains (Oryza sativa L.). A statistical model for estimating the impacts of climate change on ZEN contamination of rice grains in South Korea was constructed. Observational data on ZEN concentrations in rice grains at harvest and local weather information from 241 rice fields in South Korea were collected. To estimate the impact of weather variables on ZEN concentrations, multiple regression analyses were conducted along with variable selection procedure. The final model included the following variables: average temperature and humidity over the flowering period, daily (between days) change in temperature over the harvest period, degree of milling, and the climate region. On the basis of this regression model, maps showing ZEN contamination were produced for South Korea in the present day, the 2030s, and the 2050s, using the representative concentration pathway (RCP) emission scenarios RCP 2.6, 4.5, and 8.5. The predictive maps project that in the 2030s and 2050s, ZEN contamination in rice grains will increase nationwide, particularly more so on the western side of South Korea. Our research results might be helpful in developing effective control measures against ZEN contamination due to climate change.