Few studies have reported on the increase in cervical cancer incidence in Japan. We aimed to determine the relevant trends in the metropolitan regions of Japan and to identify the population with the highest risk, based on histological subtype, cancer stage, and diagnostic processes. Using population-based data (2009–2013), we identified 2110 women, aged ≥20 years, with cervical cancer. We estimated the age-standardized and age-specific incidence rates of cervical cancer for the study period based on the 1985 national model population. The average annual percent change (AAPC) and 95% confidence interval (CI) were calculated using the joinpoint regression analysis. We stratified the analyses based on histological subtypes, stage, and diagnostic process via cancer screening. The increase in the overall age-standardized incidence was not significant. However, the increase was significant for women aged 30–39 years (AAPC 20.0%/year, 95% CI: 9.9–31.1), which was attributable to the increase in the incidence of the squamous cell carcinoma (SCC) subtype (AAPC 23.1%/year, 95% CI: 10.7–36.8). Among younger women, aged <50 years, further stratification showed an increase in the undiagnosed early-stage SCC subtype via cancer screening. In Japan, the incidence of HPV-related cervical cancer has been increasing in undiagnosed younger women.