Dense breast is one of the strong risk factors for breast cancer among women. While it has been established that physical activity is associated with decreased risk for breast cancer, results have been inconsistent in terms of mammographic density. Thus, we examined physical activity in relation to mammographic density among Japanese women in Tokyo. We used 123,026 records from 33,698 Japanese women without a history of breast cancer who got mammograms at St. Luke's International Hospital in Tokyo, Japan from 2004 to 2019. Mammographic density was classified according to the Breast Imaging Reporting and Data System (BI-RADS), and women self-reported their physical activity level over the past year. ORs were estimated using logistic generalized estimating equations after adjusting for age, body mass index, menopausal status, parity, family history of breast or ovarian cancer, hormone therapy use, smoking status, alcohol consumption, and year. We observed inverse associations of physical activity with dense breasts. Adjusted ORs were 0.96 (95% confidence interval: 0.91-1.00) for women with physical exercise for 1-2 days per week, 0.94 (0.88-0.99) for those with physical exercise for 3-5 days per week, and 0.91 (0.84-0.99) for those with daily physical exercise when compared with those reported seldom physical exercise. Higher levels of physical activity may be associated with decreased mammographic density levels in Japanese women. Increasing physical activity may serve as a reasonable intervention to reduce mammographic density, and thereby, to mitigate the risk of breast cancer in Asian women.