This study performed flood analysis, considering the water storage of irrigation reservoirs, to realize flood control by reservoirs, which are traditional irrigation facilities. The effect on flood control was determined through flood analysis performed by varying the reservoir storage rates. Based on the flood analysis results, Japan’s flood damage costs were estimated. Using three Shared Socioeconomic Pathways (SSPs) (SSP1-2.6, SSP2-4.5, and SSP5-8.5), we evaluated the flood control potential of reservoirs under future climate conditions. When the reservoirs were empty, the damage cost reduction rate resulting from the use of reservoirs across Japan was small, ranging from 1.1% to 2.3%, but as the damage cost reduction rate did not change under all future scenarios, reductions in flood damage were not affected by changes in rainfall under future climate conditions. Moreover, some prefectures showed high damage cost reduction effects. In northern part of Japan and numerous prefectures in western Japan, the potential to reduce damage through flood control by irrigation reservoirs was high. Some prefectures experienced similar reduction levels as those under alternative adaptation strategies. In the Kanto region, flood control by irrigation reservoirs had low potential for reducing damages. Even among prefectures with low water storage capacities of irrigation reservoirs, the potential to mitigate the effect of damage was high.