Objectives: This study conducted an age-period-cohort (APC) analysis of trends in healthy lifestyle behaviors in Japan. Methods: We used National Health and Nutrition Survey data on salt intake and prevalence of smoking, drinking, and physical activity between 1995 and 2018 in Japan. Age groups were defined from 20 to 69 years old in 10-year increments. Cohorts were defined for each age group of each year with a 1-year shift, and cohorts born in 1926-1935 (first cohort) until 1989-1998 (last cohort) were examined. We conducted a Bayesian APC analysis, calculating estimated values for each behavior by age group, period, and cohort. Results: Estimated salt intake decreased from cohorts born in the 1930s to the 1960s, but increased thereafter in both sexes, and the magnitude of increase was larger for men. Estimated smoking prevalence increased in the cohorts starting from the 1930s for men and the 1940s for women, and then decreased starting in the cohorts born in the 1970s for both sexes. Although estimated drinking prevalence decreased starting in the cohorts born in approximately 1960 for men, for women it increased until the cohorts born in approximately 1970. Estimated physical activity prevalence decreased starting in the cohorts born in the 1940s in both sexes, but the magnitude of decrease was larger for women. Conclusions: Trends in cohort effects differed by sex, which might be related to changes in the social environment for women. Improvements in dietary and exercise habits are required in more recently born cohorts of both sexes.