Abstract Background Recent studies have found that long-term changes in weight during adulthood are associated with a high risk of mortality. The objective of this study was to characterize body mass index (BMI) trajectories during adulthood and to examine the association between BMI trajectories and risk of death in the Japanese population. Methods The data were extracted from Japan Public Health Center-based Prospective Study—a population-based prospective cohort study in Japan with participants aged 40–69 years followed over 20 years. The participants were categorized into multiple BMI trajectory groups using the latent class growth model. The Cox proportional-hazards model was conducted using all-cause mortality and cause-specific mortality as outcomes and the identified BMI trajectory groups as a predictor. In total, 65 520 participants were included in the analysis. Results Six BMI trajectory groups were identified: underweight stable (Group 1), low-to-high normal (Group 2), high-to-low normal (Group 3), normal to overweight (Group 4), overweight to normal (Group 5) and normal to obese (Group 6). Our Cox models showed a higher hazard (risk) of all-cause mortality among participants in the BMI-declining groups [Group 3, adjusted hazard ratio (aHR): 1.10, 95% CI: 1.05–1.16; Group 5, aHR: 1.16, 95% CI: 1.08–1.26], underweight stable group (Group 1, aHR: 1.27, 95% CI: 1.21–1.33) and normal to obese group (Group 6, aHR: 1.22, 95% CI: 1.13–1.33) than Group 2 (low-to-high normal BMI trajectory). Conclusions Stable underweight and weight loss were associated with a high risk of mortality, both of which were uniquely observed in a Japanese population.