Evidence about the impacts of the physical activity environment on adults’ weight in the context of Asian countries is scarce. Likewise, no study exists in Asia examining whether Walk Score®—a free online walkability tool—is related to obesity. This study aimed to examine associations between multiple physical activity environment measures and Walk Score® ratings with Japanese adults’ body mass index (BMI). Data from 1073 adults in the Healthy Built Environment in Japan study were used. In 2011, participants reported their height and weight. Environmental attributes, including population density, intersection density, density of physical activity facilities, access to public transportation, and availability of sidewalks, were calculated using Geographic Information Systems. Walk Scores® ratings were obtained from the website. Multiple linear regression analysis was conducted to examine the association between each environmental attribute and BMI. Adjusting for covariates, all physical activity environmental attributes were negatively associated with BMI. Similarly, an increase of one standard deviation of Walk Score® was associated with a 0.29 (95% confidence interval (CI) of −0.49–−0.09) decrease in BMI. An activity-friendly built environment was associated with lower adults’ BMI in Japan. Investing in healthy community design may positively impact weight status in non-Western contexts.