ObjectiveIn Japan, the current coverage rate of human papillomavirus (HPV) vaccination is only 30%, and the rate of biennial cervical screening is 40%. The Japanese Government has attempted to increase the coverage of HPV vaccination and cervical screening. We analyzed the cost‐effectiveness of the 9‐valent HPV vaccine and cervical screening in Japan.MethodsA yearly cycle Markov model with 15 health states was created to evaluate the cost‐effectiveness of the 9‐valent HPV vaccination and cervical screening in women aged 12–75 years. We considered four scenarios: 30% coverage of vaccination with 40% coverage of biennial screening (Scenario 1 representing the current Japanese situation), 70% (the highest proportion in 2013 in Japan) and 90% coverage of vaccination with 40% coverage of biennial screening (Scenarios 2 and 3, respectively), and 90% coverage of vaccination with 70% coverage of biennial screening (Scenarios 4). The incremental cost‐effectiveness ratio (ICER) was calculated as costs per quality‐adjusted life year (QALY) based on the perspective of the healthcare payer and compared with the benchmark for willingness to pay in Japan (41 700 USD per QALY). The cumulative morbidity and mortality in each scenario were analyzed using the Markov model.ResultsCompared with Scenario 1, the ICERs of Scenarios 2, 3, and 4 were 5382, 5321, and 8524 USD/QALY, respectively, which were lower than the benchmark for willingness to pay. As the coverage of HPV vaccination and cervical screening increased, the cumulative morbidity and mortality decreased.ConclusionIncreasing the coverage of the 9‐valent HPV vaccination and cervical screening is cost‐effective in Japan.