In the previous century, Japan rose from poverty and destruction. High levels of social inequalities before World War II were greatly equalized in the 1960–1980 period. Population health, indicated by life expectancy, height, mortality, and self-rated health, improved. Health inequalities were reduced in line with these improvements. In the past 30 years Japan has experienced low economic growth, rapid ageing, and resource constraints, with some widening of income inequalities. All are indicators of a challenging population health situation. However, health inequalities narrowed for a period in the 1990s and the early 2000s. Limited evidence suggests health inequalities have widened in recent years. Narrowing health inequality after 1990 was partly the result of worsening health in high socioeconomic groups. In the past, the combination of social structure, economic growth, culture, and social policies resulted in remarkable health development and limited health inequalities. Increased research and monitoring is needed to understand these trends, and to support policy development to reduce health inequalities as Japan changes.