BACKGROUND: Climate change has marked implications for the burden of infectious diseases. However, no studies have estimated future projections of climate change–related excess morbidity due to diarrhea according to climate change scenarios. OBJECTIVES: We aimed to examine temperature-infectious gastroenteritis associations throughout Japan and project temperature-related morbidity concomitant with climate change for the 2090s. METHODS: Weekly time series of average temperature and morbidity for infectious gastroenteritis cases in the period 2005-2015 were collated from the 47 Japanese prefectures. A two-stage time-series analysis was adopted to estimate temperature-infectious gastroenteritis relationships. Time series of present and future average daily temperature fluctuations were projected for the four climate change scenarios of representative concentration pathways (RCPs) according to five general circulation models. Excess morbidity for high and low temperatures and the net change in the period 1990–2099 were projected for each climate change scenario by assuming the absence of adaptation and population alterations. RESULTS: In the period 2005–2015, 11,529,833 infectious gastroenteritis cases were reported. There were net reductions in temperature-induced excess morbidity under higher emission scenarios. The net change in the projection period 2090-2099 in comparison with 2010–2019 was [Formula: see text] (95% empirical confidence interval [eCI]: [Formula: see text], 0.5) for RCP2.6, [Formula: see text] (95% eCI: [Formula: see text], [Formula: see text]) for RCP4.5, [Formula: see text] (95% eCI: [Formula: see text], [Formula: see text]) for RCP6.0, and [Formula: see text] (95% eCI: [Formula: see text], [Formula: see text]) for RCP8.5, and the higher the emissions scenario, the larger the estimates reductions. Spatial heterogeneity in the temperature-morbidity relationship was observed among prefectures (Cochran Q test, [Formula: see text]; [Formula: see text]). CONCLUSIONS: Japan may experience a net reduction in temperature-related excess morbidity due to infectious gastroenteritis in higher emission scenarios. These results might be because the majority of temperature-related diarrhea cases in Japan are attributable to viral infections during the winter season. Further projections of specific pathogen-induced infectious gastroenteritis due to climate change are warranted. https://doi.org/10.1289/EHP4731.