Background: Cognitive and academic outcomes in children with epilepsy are influenced by both disease severity and treatment intensity. The effect of increasing antiepileptic drug burden on school performance remains a critical clinical concern. Aim: To evaluate the relationship between the number of antiepileptic drugs and school performance in children aged 7–12 years with epilepsy. Patients and Methods: A cross-sectional analytical study was conducted on 174 children with epilepsy. Participants were categorized into three groups according to treatment type: monotherapy (n = 70), dual therapy (n = 60), and triple therapy (n = 44). School performance scores were compared across groups. Seizure control (good, moderate, poor) and age categories were also analyzed. Results: A marked decline in school performance was observed with increasing drug burden. Children on monotherapy showed the highest mean scores, followed by dual therapy, while triple therapy demonstrated the lowest performance (F = 566.201, p = 0.000000). Seizure control significantly influenced outcomes, with good control associated with higher scores compared to moderate and poor control (F = 73.457, p = 0.000000). A significant interaction between treatment type and seizure control was identified (F = 128.773, p = 0.000000), indicating that the effect of therapy varied depending on seizure status. No significant differences were observed across age groups (F = 1.009, p = 0.366757). A very strong negative correlation was detected between the number of antiepileptic drugs and school performance (r = -0.932, p = 0.000000). Multiple regression analysis confirmed that drug burden and seizure control were independent predictors of academic performance (R2 = 0.873, p = 0.000000). Additionally, seizure control distribution differed significantly across treatment groups (χ2 = 88.711, p = 0.000000). Conclusion: Increasing antiepileptic drug burden is strongly associated with reduced academic performance in children with epilepsy. This effect is compounded by seizure control status, highlighting the need for optimized therapeutic strategies that balance seizure management with cognitive outcomes.