Migraine involves 5-10% of children and adolescents. Thirty percent of children with severe migraine attacks have school absence and reduced quality of life that need preventive therapy. The purpose of this randomised control trial study is to compare the effectiveness, safety and the tolerability of pregabalin toward Propranolol in migraine prophylaxis of children. From May 2011 to October 2012, 99 children 3-15 years referred to the neurology clinic of Mofid Children's Hospital with a diagnosis of migraine enrolled the study. Patients randomly divided into two groups (A&B). We treated children of group A with capsule of pregabalin as children of group B with tablet of propranolol for at least 8 weeks. In this study, 99 patients were examined that 91 children reached the last stage. The group A consistsed of 46 patients, 12(26.1%) girls, 34 (73.9%) boys and the group B consisted of 45 patients, 14(31.1%) girls, 31 (68.9%) boys. Basis of age, gender, headache onset, headache frequency, migraine type, triggering and relieving factors there was no significant difference among these groups (P>0.05). After 4 and 8 weeks of Pregabalin usage monthly headache frequency decreased to 2.2±4.5 and 1.76±6.2 respectively. Propranolol reduced monthly headache frequency up to 3.73±6.11 and 3.34±5.95 later 4 and 8 weeks respectively. There was a significant difference between these two groups according to headache frequency reduction (P=0.04). Pregabalin efficacy in reducing the frequency and duration of pediatric migraine headache is considerable in comparison with propranolol.