Recently, growing attention has been paid to the changes of brain biomarkers following the epilepsy. However, establishing specific epilepsy-related biomarkers has been impeded due to contradictory findings. This study systematically reviewed the evidence on brain biomarkers in epilepsy and determined reliable biomarkers in epileptic patients. A comprehensive systematic search of online databases was performed to find eligible studies up to August 2019. The quality of studies methodologically was assessed using the Newcastle-Ottawa Scale score. Among the several biomarkers, S100 calcium binding protein B (S100B) and neuron specific enolase (NSE) have been qualified for meta-analysis of the association between epilepsy and the brain biomarkers. Inverse-variance weights method was used to calculate pooled standardized mean difference (SMD) estimate with 95% CI, and random effects meta-analysis was conducted taking into account conceptual heterogeneity. Sensitivity analysis and publication bias assessment was performed using Stata. Of 29 studies that were qualified for further analysis, only 22 studies were eligible to quantify by meta-analysis. Significant increase of serum S100B levels (SMD = 0.80; 95% CI 0.18 to 1.42) but not NSE (SMD = 0.45; 95% CI -0.09 to 1.00) has been found in epileptic patients compared with healthy controls. Subgroup meta-analysis by age demonstrated that S100B could be found in pediatric (SMD = 1.15; 95% CI 0.03 to 2.27) not adult patients (SMD = 0.43; 95% CI -0.12 to 0.98). Findings of this meta-analysis indicate that serum level of S100B is significantly increased in epileptic patients, suggesting the elevation and release of the brain biomarkers from brain to blood following epileptic seizures.