Introduction: Adverse drug events (ADEs) are a major cause of mortality. Objective: We examined long-term trends for ADE-related deaths in Japan. Methods: This observational study was conducted using the Japanese Vital Statistics from 1999 to 2016. Data for all ADE-related deaths were extracted using International Classification of Diseases, Tenth Revision codes. We analysed ADE-related deaths by age and sex and calculated crude and age-standardised mortality rates (ASMR) per 100,000 people. We used Joinpoint regression analysis to identify significant changing points in mortality trends and to estimate annual percentage change (APC). Results: In total, 16,417 ADE-related deaths were identified. The crude mortality rate for individuals aged ≥ 65 years was higher than that of young individuals. The ASMR per 100,000 people increased from 0.44 in 1999 to 0.64 in 2016. The crude mortality rate increased from 0.44 in 1999 to 1.01 in 2016. The APC of ASMR increased at a rate of 2.8% (95% confidence interval [CI] 1.4–4.2) throughout the study period. In addition, crude mortality increased at a rate of 5.7% (95% CI 4.2–7.3) annually from 1999 to 2016. The ADE-related mortality rate was higher for men than for women during the study period. Conclusions: The number of and trend in ADE-related deaths increased in Japan from 1999 to 2016, particularly in the older population.