Objective To explore the levels and clinical significance of Brain-Derived Neurotrophic Factor (BDNF), S100β protein, and B-Cell Activating Factor (BAFF) in pediatric patients treated with a combination of levetiracetam and lamotrigine for epilepsy.Methods A retrospective review was conducted on 106 pediatric epilepsy patients treated at our hospital from January 2020 to December 2023. Patients were divided into an observation group of 56 patients treated with both levetiracetam and lamotrigine, and a control group of 50 patients treated with levetiracetam alone. The study compared the treatment efficacy, levels of BDNF, S100β, and BAFF in peripheral blood, and the Montreal Cognitive Assessment (MoCA) scores between two groups of children. The analysis included correlating the levels of BDNF, S100β, and BAFF with treatment outcomes.Results The overall effectiveness of the study group was higher than that of the control group (P <0.05). The differences in BDNF, S100β and BAFF levels before and after treatment in the study group were higher than those in the control group (P <0.05). The differences in the number of epileptic seizures, duration of epileptic seizures, and MoCA scores before and after treatment were all higher in the study group than in the control group (P <0.05). After treatment, the levels of BDNF (r_s =0.301, P =0.002), BAFF (r_s =0.346, P =0.000) in the study group were positively correlated with treatment efficacy, and S100β (r_s =-0.405, P =0.000) was negatively correlated with treatment efficacy.Conclusion Treatment with levetiracetam combined with lamotrigine significantly increased levels of BDNF and BAFF in the peripheral blood of children with epilepsy, while levels of S100β showed a decreasing trend. These biomarkers' changes are closely associated with the treatment outcomes of epilepsy.