Objective: The present study aimed to examine the prevalence of dyscalculia, dyslexia, and their comorbidity rates in a large population-based sample of children with idiopathic epilepsy (N = 2282) and a comparison sample of typically developing schoolchildren (N = 2371). Methods: Both groups of children were screened using an arithmetic fluency test for dyscalculia and a reading fluency test for dyslexia. Their comorbidity rates were assessed. The prevalence rates of dyscalculia, dyslexia, comorbidity, and isolated dyscalculia/dyslexia (ie, participants with comorbid dyslexia and dyscalculia were excluded) were analyzed. Results: In both −1.5 SD and −1 SD cutoff criterion, the prevalence rates were about two times higher in children with idiopathic epilepsy than in other schoolchildren; the prevalence rates of isolated dyslexia were higher in children with idiopathic epilepsy than in other schoolchildren (−1 SD: 10.9% vs 8.6%; −1.5 SD: 6.5% vs 4.7%). Meanwhile, comorbidity rates of dyscalculia and dyslexia were higher in children with idiopathic epilepsy than in other schoolchildren (32.7% vs 26.6%; 38.3% vs 23.5%, respectively). Overall, patterns of prevalence rates were different for children with idiopathic epilepsy and schoolchildren, in which children with idiopathic epilepsy had a higher prevalence rate of dyscalculia than dyslexia, while schoolchildren had a higher prevalence of dyslexia than dyscalculia, regardless of cutoff criteria. Interestingly, gender differences in the prevalence rates of all types of learning disabilities were found in schoolchildren, but there were only gender differences in the prevalence rates of dyslexia in children with idiopathic epilepsy. Significance: The results highlight the vulnerability of children with idiopathic epilepsy for learning disabilities and a differential pattern of gender differences in dyslexia. Moreover, different patterns of prevalence rates suggest that children with idiopathic epilepsy and schoolchildren are more prone to different types of learning disabilities. The findings suggest needs for special interventions of learning disabilities for children with idiopathic epilepsy.