Abstract Backgrounds Eosinophilic esophagitis (EoE) has been increasingly diagnosed in Western countries whilst there have been few general population-based studies in Asia. In addition, risk factors for EoE have not been examined completely. The aim of the study was to investigate the epidemiology and risk factors of EoE in Japanese general population. Methods We analyzed an employer-based health insurance claim database from January 2005 to September 2022. EoE cases were identified based on the International Classification of Diseases-tenth Revision code, K20.0. We calculated the incidence and prevalence of EoE using Poisson regression and binomial distribution with exact methods respectively. Using 10 times more matched controls for EoE cases, a nested case-control study identified potential risk factors for adult EoE. Results Of 15,200,895 individuals, 1,010 EoE cases were identified. The incidence and prevalence of EoE were 2.82 (95% CI 2.44–3.26) per 100,000 person-years and 10.68 (95% CI 10.01–11.37) per 100,000 people in 2022. Both rates had dramatically increased since 2017. smoking was associated with a 59% risk reduction of EoE whereas constant alcohol consumption was associated with a 63% increase in the risk of EoE. EoE was not associated with either body mass index or health-related diseases such as hypertension, diabetes mellitus, hyperuricemia, and dyslipidemia. Conclusion The incidence and prevalence of EoE in Japan has steadily increased over the past two decades. Nevertheless, EoE remains less common in Japan compared to Western countries. Factors contributing to the epidemiology of EoE on a global basis may improve our understanding of the contribution of genetic and environmental risk factors. In light of potential risk factors, further study is warranted to investigate whether lifestyle intervention can improve the management of EoE.