Introduction: Human health and wellbeing may depend on economic growth, the implication being that policymakers need to choose between population health and the health of ecosystems. Over two decades of low economic growth, Japan's life expectancy grew. Here we assess the temporal changes of subjective health and health inequality during the long-term low economic growth period. Methods: Eight triennial cross-sectional nationally representative surveys in Japan over the period of economic stagnation from 1992 to 2013 were used (n = 625,262). Health is defined positively as wellbeing, and negatively as poor health, based on self-rated health. We used Slope and Relative Indices of Inequality to model inequalities in self-rated health based on household income. Temporal changes in health and health inequalities over time were examined separately for children/adolescents, working-age adults, young-old and old-old.Results: At the end of the period of economic stagnation (2013), compared to the beginning (1992), the overall prevalence of wellbeing declined slightly in all age groups. However, poor health was stable or declined in the young-old and old-old, respectively, and increased only in working-age adults (Prevalence ratio: 1.14, 95% CI 1.08, 1.20, <0.001). Over time, inequality in wellbeing and poor self-rated health were observed in adults but less consistently for children, but the inequalities did not widen in any age group between the start and end of the stagnation period.Conclusions: Although this study was a case study of one country, Japan, and inference to other countries cannot be made with certainty, the findings provide evidence that low economic growth over two decades did not inevitably translate to unfavourable population health. Japanese health inequalities according to income were stable during the study period. Therefore, this study highlighted the possibility that for high-income countries, low economic growth may be compatible with good population health.