Cyclic vomiting syndrome (CVS) is a gastrointestinal disorder that is characterized by recurrent episodes of vomiting. Previous studies have provided reliable data on the prevalence of CVS among children in Japan; however, neither prevalence data nor incidence of CVS is available for adults. Hence, we obtained detailed prevalence and incidence data for CVS and estimated the total number of CVS cases in Japan. This retrospective cross-sectional study was conducted using the JMDC (JMDC, Inc.; formerly known as Japan Medical Data Center Co., Ltd.,) database, which is a de-identified Japanese claims database. Individuals enrolled between January 2017 and December 2017 were included in this study. Longitudinal data for eligible populations were used to identify patients who displayed CVS symptoms throughout the follow-up period. Due to the lack of a specific diagnosis code for CVS in 2017, the Rome IV criteria were applied to identify CVS cases in the pediatric and adult populations. The prevalence was standardized to the 2017 Japanese census and extrapolated to estimate the number of CVS cases. A total of 2,093 patients with CVS were identified from 3,506,144 individuals. The overall age-and-sex-standardized prevalence was 0.32 per 1,000 population (95% confidence interval [CI]: 0.30-0.34), projected to approximately 49,000 patients with CVS across Japan. The pediatric age-and-sex-standardized prevalence was 2.10 per 1,000 population (95% CI: 2.01-2.19), and the adult prevalence was 0.05 per 1,000 population (95% CI: 0.04-0.06). Marked sex differences were observed before and after 12 years of age. Thus our study provides the first large-population-based estimates of CVS prevalence and incidence in Japan, and currently, the only estimates for adult CVS in Japan.