Aim Although the modification of lifestyle factors might facilitate weight control, the effects of health behaviors on the trajectory of bodyweight among older adults have been understudied. We examined the effect of changes in smoking, alcohol use and physical activity on the long‐term trajectory of body mass index (BMI) among older Japanese adults. Methods Data came from a national sample of 4869 Japanese adults aged 60 years and older at baseline, with up to seven repeated observations over a period of 19 years (1987–2006). Hierarchical linear modeling was used to analyze the intrapersonal and interpersonal differences in BMI trajectory. Results The average BMI among older Japanese adults was 22.3 at baseline, and decreased with an accelerating rate over time. Smoking was significantly associated with lower BMI over time, whereas smoking cessation was associated with higher BMI. Drinking and physical activity were not associated with BMI. We found significant interactions between age and smoking status, and between sex and physical activity, on BMI trajectory: the association between smoking and lower BMI was stronger in younger participants compared with older participants. The association between physical activity and higher BMI was more pronounced among men compared with women. Conclusion The present findings yield important new information regarding the complex dynamics underlying the linkage between lifestyles factors and BMI trajectory among older Japanese, and suggest that there might be cross‐cultural differences in these linkages. Geriatr Gerontol Int 2017; ••: ••–••.