Objectives: This study aimed to analyze smoking prevalence trends in urban and non-urban areas using age-period-cohort (APC) analysis. Methods: Data on smoking prevalence from 2004 to 2019 were extracted from the Comprehensive Survey of Living Conditions in Japan. Government ordinance-designated cities and the special wards in Tokyo were defined as urban areas. The respondents ranged from 20-79 years old, grouped in five-year increments. Cohorts were defined for each age group of each year, and those born between 1925-1929 and 1995-1999 were examined. We calculated the estimated smoking prevalence for each age, period, and cohort, as well as the smoking prevalence ratio of non-urban areas compared with urban areas from the APC analysis result. Results: The degree of decrease of the period effects on smoking prevalence was larger in urban areas than in non-urban areas for both men and women. Also, the smoking prevalence ratio for non-urban areas compared with that of urban areas was most of the times above 1for men, except in the older age groups. In addition, the prevalence ratio between the areas decreased, particularly with an increase in age. For women, although the smoking prevalence ratio in non-urban areas compared to urban areas was below 1 until cohorts born in the 1970s, the trend reversed thereafter. Conclusions: The result of this study therefore suggested that further smoking control and cessation measures are necessary, particularly for older cohorts in urban women and for younger ages in non-urban men.