OBJECTIVE To investigate the preventive effect of behavioral therapy plus flunarizine in children with migraine. METHODS Ninety pediatric patients with migraine between January 2011and January 2014 were randomly divided into treatment group (45 cases) and control group (45 cases). The treatment group received behavioral therapy in addition to oral flunarizine, while the control group received oral flunarizine alone. All patients were followed up for 3 months to evaluate the therapeutic effect by the Pediatric Migraine Disability Assessment Score (PedMIDAS) and improved Bussone headache index. RESULTS There were no significant differences in PedMIDAS (P>0.05) and improved Bussone headache index (P>0.05) between the control and treatment groups before treatment. Significant differences were observed in PedMIDAS (16±8 vs 20±10; P<0.05) and improved Bussone headache index (25±18 vs 37±21; P<0.05) between the two groups after 3 months of treatment. CONCLUSIONS Preventive treatment of behavioral therapy plus oral flunarizine shows a better clinical efficacy than oral flunarizine alone in children with migraine and holds promise for clinical application.