•Over thirty years of temperature-mortality data in Japan were analyzed to understand population adaptation to heat.•We examined if changes in adaptation are associated with air conditioning prevalence, healthcare, and socioeconomic profiles.•Excess heat mortality has declined over the past few decades in Japan, but the mortality impact of heat remains significant.•Socioeconomic developments over time positively influenced the reduction of heat-related mortality risk.•Future research should focus on the challenges of specific adaptation measures at the local context. Excessive heat is a health risk, yet previous studies have observed a general decline in sensitivity to heat despite increasing temperatures. Conclusive evidence is lacking on whether long-term changes of this sensitivity can be attributed to specific adaptation measures, such as air conditioning, or should be linked to societal adaptation, such as improved healthcare systems or socioeconomic well-being. The aim of this study was to assess the variation of the association between heat and daily mortality during summer in Japan since the 1970s and to examine the influence of air conditioning (AC) prevalence, healthcare resources, and socioeconomic developments at the prefecture level on this variation. We analyzed daily total, cardiovascular and respiratory disease mortality and temperature data from 1972 to 2010 for 47 prefectures. We used Poisson generalized linear model to estimate the effect of heat on mortality, random effects model to obtain the mean national effect estimates, and meta-regression to explore the impact of prefecture-level characteristics. Average summer temperature has increased across Japan during the 39-year period. Excess mortality attributable to summer heat has decreased, with a national reduction of 20 (95%CI: 17, 22), 21 (95%CI: 18, 25), and 46 (95%CI: 36, 55) cases of total, cardiovascular, and respiratory deaths (per 1000 deaths). The increase of AC prevalence was not associated with a reduction of excess mortality over time. Prefectures and populations with improved economic status documented a larger decline of excess mortality. Healthcare resources were associated with fewer heat-related deaths in the 1970s, but the associations did not persist in the more recent period (i.e., 2006–2010). Excess mortality due to heat has reduced in Japan, suggesting population adaptation. Yet, heat remains a significant health risk. Socioeconomic developments may play a role in heat adaptation. These findings may have implications for ensuring effective prevention of heat-related health impacts.