Background: Although school-age children with epilepsy are at a high risk of developing comorbid learning disabilities, there is a lack of empirical research to confirm the prevalence of learning disabilities among children with idiopathic epilepsy in China. Further, previous research has not confirmed whether children with epilepsy have a higher prevalence rate of learning disabilities than other school-age children. Methods: The current study aims to examine the prevalence and gender ratios of dyscalculia, dyslexia, and comorbidity among children with idiopathic epilepsy and other school-age children in China. Specific screening tests in arithmetic fluency (dyscalculia), reading fluency (dyslexia), and their co-occurrence were administered in a large population-based sample of children with epilepsy (N = 2,282) and other school-age children (N = 2,371). The prevalence of dyscalculia, dyslexia and comorbidity were calculated based on three cutoff criteria. Findings: The results showed that children with idiopathic epilepsy, when compared to other school-age children, have significantly higher prevalence rate of dyscalculia (-1 SD cutoff: 7·6% vs. 3·8%, -1·5 SD cutoff: 4·1% vs. 2·4%), dyslexia (-1 SD cutoff: 9·0% vs. 3·7%, -1·5 SD cutoff: 3·9% vs. 2·0%) and comorbidity (-1 SD cutoff: 5·1% vs. 1·4%, -1·5 SD cutoff: 1·5% vs. 0·4%, -2 SD cutoff: 0·4% vs. 0·1%). Moreover, gender differences in the prevalence rate of dyslexia only appeared among other school-age children. Interpretation: The results suggest that children with idiopathic epilepsy are more vulnerable to dyscalculia and dyslexia compared to other school-age children. Risk factors in the idiopathic epilepsy population should be identified to formulate effective prevention strategies. Moreover, gender differences on the prevalence of dyscalculia, dyslexia and comorbidity only exist among typical school-age children, which might be explained by clinical factors related to idiopathic epilepsy, therefore, future studies could make further examination. Funding: Funding Natural Science Foundation of China (Grant No. 31700977, 31671151), Natural Science Foundation of Beijing (Grant No. 5212004), The 111 Project (Grant No. BP0719032), Advanced Innovation Center for Future Education (Grant No. 27900-110631111), Directional Guidance Fund for the Capital Institute of Pediatrics (Grant No. FX-2019-03). Declaration of Interest: We declare no competing interests. Ethical Approval: This study was approved by the Human Research Ethics Committee at the Capital Institute of Pediatrics (approval no.: SHERLL 2019001). We also obtained oral consent from participants and informed consent signed by their guardians.