Purpose: Trends of epilepsy in children were correlated with febrile seizure (FS) in a previous retrospective study. In the present study, the authors obtained relevant data from a nationwide cohort database to investigate trends in subsequent epilepsy in children with a history of recurrent FS. Methods: A total of 10,210 children with FS comprised the cohort. The diagnosis date was used as the index date. A comparison cohort was randomly matched with each case based on age, sex, urbanization level, parents’ occupation, and index date. Cox proportional hazard regression was performed to estimate the hazard ratio and confidence interval of FS-associated epilepsy. Results: This retrospective cohort study included 7729 children with FS and a comparison cohort of 30,916 children. The incidence of epilepsy was 11.4-fold higher in the FS cohort than in the comparison cohort (5.67 vs. 0.49 per 1000 person-years, respectively). Compared with the comparison cohort, the epilepsy incidence rate ratio increased in children with admissions for FS, from 8.62 at 1 admission to 26.2 at ≥2 admissions (95% CI 6.80–10.9, and 19.78–34.8, respectively; p for trend < 0.0001). Conclusion: FS may increase the risk for subsequent epilepsy in children. Recurrent FS increased the cumulative incidence of epilepsy.