Academic self-concept could significantly affect academic achievement and self-confidence in children with epilepsy. However, limited attention has been devoted to determining factors influencing academic self-concept of children with epilepsy. We aimed to analyze potentially significant variables (gender, frequency of seizures, duration of epilepsy, intellectual disability, learning disability and attention deficit hyperactivity disorder) in relation to academic self-concept in children with epilepsy and to additional domains of their quality of life. The study group consisted of 182 children and adolescents aged 9–14 years who completed the SPAS (Student's Perception of Ability Scale) questionnaire determining their academic self-concept and the modified Czech version of the CHEQOL-25 (Health-Related Quality of Life Measure for Children with Epilepsy) questionnaire evaluating their health-related quality of life. Using regression analysis, we identified learning disability as a key predictor for academic-self concept of children with epilepsy. While children with epilepsy and with no learning disability exhibited results comparable to children without epilepsy, participants with epilepsy and some learning disability scored significantly lower in almost all domains of academic self-concept. We moreover found that children with epilepsy and learning disability have significantly lower quality of life in intrapersonal and interpersonal domains. In contrast to children with epilepsy and with no learning disability, these participants have practically no correlation between their quality of life and academic self-concept. Our findings suggest that considerable attention should be paid to children having both epilepsy and learning disability. It should comprise services of specialized counselors and teaching assistants with an appropriate knowledge of epilepsy and ability to empathize with these children as well as educational interventions focused on their teachers and classmates.