Objective: Human papillomavirus (HPV) vaccination was introduced in Japan in April 2013, as a national immunization program for girls aged 12–16 years, after an initial introduction in 2010 as a public-aid program for girls aged 13–16 years. The Yuri-Honjo district had the highest vaccine coverage among women aged 17–51 years in 2017, due to the original public-aid program. The aim of this study was to evaluate the differences in the vaccine types of HPV16/18 infections between 2008–2012 (pre-vaccine era) and 2013–2017 (vaccine era).Materials and Methods: We evaluated whether HPV vaccination was associated with a decrease in the prevalence of HPV16/18 and high-risk HPV and the incidence of HPV-associated cervical lesions. A total of 1,342 women aged 18–49 years, covering both the pre-vaccine and vaccine eras, who visited Yuri Kumiai General Hospital and underwent HPV genotype tests from June 2008 to December 2017 were compared.Results: Among women aged 18–24 years with higher vaccine coverage (68.2%), the prevalence of HPV16/18 and high-risk HPV decreased from 36.7% and 69.4%, respectively, in the pre-vaccine era to 5.8% and 50.0%, respectively, in the vaccine era (p=0.00013 and p=0.047, respectively). Among those with cervical intraepithelial neoplasia grade 2− and grade 2+, HPV16/18 prevalence decreased from 30.0% to 2.7% (p=0.0018) and from 81.8% to 36.4% (p=0.030), respectively. In this age group, the rate of HPV16/18 positivity decreased significantly. Among age groups with lower vaccine coverage, HPV prevalence did not significantly differ between the two eras.Conclusion: The prevalence of HPV16/18 and high-risk HPV significantly decreased in women aged 18–24 years, most of whom were vaccinated. HPV vaccination effectively reduced the prevalence of HPV16/18 infections in the Yuri-Honjo district.