Migraine is the most common acute primary headache in children and adolescents. In 2014, topiramate became the first preventive drug for migraine, approved by the Food and Drug Administration (FDA) for adolescents. This meta-analysis was aimed to evaluate the efficacy and safety of topiramate in the prevention of pediatric migraine. We searched the PubMed, EMBASE, Cochrane Library, and Chinese National Knowledge Infrastructure (CNKI) databases up to June 2019 for eligible randomized controlled trials (RCTs). The primary outcomes were mean migraine days per month, ≥50% reduction rate, and Pediatric Migraine Disability Assessment Scale (PedMIDAS) scores. RevMan5.3 software was performed for statistical analysis. Overall, 5 RCTs recruiting 531 patients (6-17 years of age) were included in the meta-analysis. The target dose of topiramate was 2 mg/kg (the maintenance phase was 12 weeks), 2-3 mg/kg, 50 mg/day, and 100 mg/day (maintaining for 16 weeks), respectively, in the included studies. Our results demonstrate that participants receiving topiramate had a significant advantage in remitting the monthly migraine days than those receiving placebo, with a mean difference (MD) of -0.78 ( = 531; 95% CI, -1.23 to -0.32; = 3.37; = 0.0008). Topiramate could also reduce the mean PedMIDAS scores ( = 238; 95% CI, -16.53 to -0.49; = 2.43; = 0.04). However, there was no significant difference in the percentage of patients experiencing a ≥50% reduction in monthly headache days between topiramate and placebo groups ( = 531; 95% CI, 0.94-1.77; = 1.58; = 0.11). Topiramate was associated with higher rates of side effects such as weight decrease ( = 395; 95% CI, 2.73-22.98; = 3.81; < 0.01) and paresthesia ( = 531; 95% CI, 3.05-13.18; = 4.94; < 0.01). Topiramate can significantly decrease monthly headache days and migraine-related burden in migraine patients <18 years old. However, it failed to increase 50% response rate. Adverse events seem to be more frequent in topiramate-treated children.