We performed a large, population-based study to analyze the risk factors of the febrile seizures and the subsequent afebrile epileptic seizures. Methods: Relevant data from children born between 2002-2007 were retrieved from the Korean National Health Insurance Service-National Sample Cohort 2002-2013. Children who did not survive the first five years were excluded from the analysis. The risk factors for febrile seizures were assessed separately in per-person and perfebrile case analyses, and factors contributing to an increased risk of subsequent afebrile epileptic seizures were identified. Results: A total of 54,233 children were included and the five-year prevalence rate of febrile seizure was 11.19%. In the per-person analysis, male sex, preterm birth and brain injury at birth increased the risk of febrile seizure with odds ratios of 1.17, 1.40 and 1.97 (all p < 0.001), respectively. A high household income level was associated with reduced odds of febrile seizure. In the per-febrile illness analysis, male sex, brain injury at birth, presumed bacterial infection, gastrointestinal or genitourinary infection and unspecified sepsis were independent risk factors of a febrile seizure during febrile illness. The cumulative number of febrile seizure episodes, especially more than the third episodes, was associated with a new diagnosis of an afebrile epileptic seizure within one year. Conclusion: Sex, preterm birth, brain injury at birth, presumed bacterial infection, genitourinary and gastrointestinal infections and unspecified sepsis were identified as likely risk factors for febrile seizures. A greater number of febrile seizure episodes was associated with a higher probability of subsequent afebrile epileptic seizures.