Cervical cancer (CC) is one of the most common gynecological malignancies in females, mainly caused by human papillomavirus (HPV). In countries with lower HPV vaccine coverage, such as Japan, medical examination may play a key role in decreasing CC incidence. This study aimed to quantify the effect of medical examination on cervical cancer (CC) incidence in Japan, considering the effects of possible risk factors. By collecting Japan’s Prefectural data on CC incidence (2013–2017), incidence of sexually transmitted diseases (STDs; Chlamydia, Herpes, Condyloma, and Gonorrhea; 1993–2012), screening and detailed examination rate against CC (2013–2016), smoking rate (2001–2013), economic status (disposable income and economic surplus; 2014–2015), and education status (2015), we analyzed associations among them using Pearson’s correlation coefficients. Additionally, assuming that the incidence of STDs reflects the frequency of risky sexual behavior at the co-infection point with HPV, we constructed generalized linear models to predict CC incidence, taking a 5–20-year time-lag between incidences of STDs and the CC incidence. Against CC incidence, Chlamydia in females and Gonorrhea in males with a 15-year time-lag showed positive associations, while Condyloma in both genders with a 15-year time-lag, screening rate, economic status, and smoking rate showed negative associations. An increase in screening test rate by 10% was estimated to decrease CC incidence by 9.6%. This means that screening tests decrease CC incidence effectively, but not drastically, suggesting the need for additional countermeasures for CC prevention.