Stroke is the first and fourth leading cause of death in China and Japan, respectively. Physical inactivity was suggested to be one of the most important risk factors for stroke mortality. Therefore, this study aimed to assess long-term trends in stroke mortality attributable to low physical activity (LPA) in China and Japan during the period 1990-2016. Mortality data were obtained from the Global Burden of Disease Study 2016 (GBD 2016) and were analyzed with an age-period-cohort method. The age-standardized mortality rates (ASMRs) showed declining trends for LPA-attributable stroke mortality. The overall net drift per year was -1.3% for Chinese men, -2.9% for Chinese women, -3.9% for Japanese men, and -5.6% for Japanese women. In both countries, the local drift values were below zero in all age groups. The longitudinal age curves of LPA-attributable stroke mortality were higher in men than in women in all age groups. The period and cohort rate ratios showed similar downward patterns for both sexes, with a faster decline for women than for men. However, the physically active population is still small in both countries. Therefore, policymakers should further promote physical activity as one of the most recommended effective strategies in stroke prevention.