Nationwide studies investigating the association between daily mean temperature and Kawasaki disease are lacking. This study aimed to examine the association between ambient temperature and Kawasaki disease by utilizing daily data from nationwide administrative claims databases. The daily number of Kawasaki disease patients younger than 15 years old, who were hospitalized from 2011 to 2022, was extracted from the nationwide administrative claims database of hospitalizations in Japan. Daily mean temperature data and relative humidity data were obtained from the Japan Meteorological Agency. Since the exposure of interest includes heat, hospitalizations during the five warmest months (May through September) were used for analysis. A time-stratified case-crossover study with conditional quasi-Poisson regression analysis was used to estimate the relative risk (RR) of weather exposure for Kawasaki disease hospitalization with a lag of 0–5 days by prefecture. Relative humidity was included in the model simultaneously to control for its potential confounding effect. Random-effects meta-analysis was used to estimate pooled RRs. There was a total of 48,784 cases of Kawasaki disease hospitalization during the study period, of which 87.9% were under 5 years of age. Exposure to high daily mean temperatures was associated with an increased risk of hospitalization for Kawasaki disease. Specifically, exposure to extreme high daily mean temperatures (99th percentile high temperature) was associated with higher risk of hospitalization by 33% (RR 1.33, 95% confidence interval (CI):1.08, 1.65). Similar results were obtained from sensitivity analysis. Future research should elucidate the mechanisms by which high temperature is associated with hospitalization for Kawasaki disease.