Future climate change is a major threat to biodiversity through habitat degradation or species geographic range shifts. Species range shifts can affect the effectiveness of existing protected areas in the future, but the effect is largely unknown in Japan. We constructed species distribution models for butterflies and projected into different emission scenarios until 2080 to identify species that will be endangered and find priority areas for conservation. As a result, vulnerable species will increase 42 species in 2080 under the business as usual scenario, compared to 32 species in current time. These vulnerable species will shift their distributions to higher elevation areas, particularly in Honshu and the southern area. Since existing protected areas are mainly situated in mountainous areas, their hotspots will have been covered with PAs, suggesting more conservation effort on those areas. In Hokkaido, on the other hand, there will be more gaps with PAs due to the vast, cooler climate and flat topology, suggesting that to create new reserves is necessary, including privately protected areas.