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Background Sleep deprivation has notable effects on neurobehavioural functioning in children. However, the link between sleep duration and the risk of developing epilepsy in early childhood remains uncertain. The aim of this study was to explore the association between sleep duration at 12 and 18 months and the risk of epilepsy at 2 and 3 years of age.Methods Data from the Japan Environment and Children’s Study (JECS), a largescale birth cohort, were analysed. We assessed the risk of epilepsy at 2 and 3 years of age among children sleeping under 11 hours per night, the minimum recommended by the American Academy of Sleep Medicine for 1–2 year olds.Results Overall, 86 441 children were retrospectively analysed. Of these, 8786 (10.2%) and 12 850 (14.9%) slept for less than 11 hours at 12 months and 18 months, respectively. Multivariate logistic regression showed that a sleep duration of less than 11 hours at 12 months remained significantly associated with epilepsy incidence at 2 and 3 years (adjusted OR (aOR) 2.02, 95% CI 1.01 to 4.01, p=0.045; aOR 1.98, 95% CI 1.15 to 3.41, p=0.013). Furthermore, a sleep duration of less than 11 hours at 12 and 18 months was significantly associated with epilepsy incidence at 3 years (aOR 2.77, 95% CI 1.28 to 6.01, p=0.010).Conclusions Insufficient sleep in infancy may be linked to epilepsy later in childhood. These findings highlight the importance of sleep interventions during early life to improve long-term neurological health.