Herein we report the interim vaccine effectiveness (VE) of quadrivalent inactivated influenza vaccine for the 2019/2020 influenza season in Japan. We conducted a retrospective observational cohort study of 381 enrolled influenza-like illness patients aged ≥ 15 years who were examined via the rapid-influenza diagnostic test at the Ambulatory Care unit of the National Center for Global Health and Medicine in Tokyo, Japan from the beginning of October 2019 to the end of January 2020. VE was estimated using a test-negative design. VE was calculated as (1 - odds ratio) × 100%, comparing influenza A test positivity between vaccinated and unvaccinated patients. Of the 381 patients initially screened for inclusion, 314 were enrolled in the study. Of these, 105 were vaccinated, 98 were diagnosed with influenza A, and 5 were diagnosed with influenza B. Overall VE against influenza A was 27.6% (95% confidence interval [CI] -21.1 to +57.4), and in patients aged ≥ 65 years it was 47.3% (95% CI -76.0 to +86.0). Influenza vaccination can be regarded as being of continued benefit during the ongoing 2019/2020 influenza season, but further accumulation of cases and methodological consideration are necessary to estimate VE more precisely.