Introduction: Migraine headaches have a negative impact on daily living activities in children. Many children with migraine need prophylactic medications in addition to biobehavioural measures. Until now, only topiramate has been approved by the FDA (US Food and Drug Administration) as a prophylactic medication in children with migraine. However, topiramate has many unacceptable adverse cognitive effects, therefore, conducting well-designed trials to show the efficacy of safer medications has been recommended. Aim of the study: We conducted a trial to assess the efficacy and safety of levetiracetam in the prophylaxis of migraine headaches in children. Material and methods: In an open-label, randomised, controlled trial, we assessed the efficacy and safety of levetiracetam in the prophylaxis of migraine headaches in children compared to a well-known prophylactic agent, amitriptyline. The primary outcome measure was reduction of monthly headache frequency. The secondary outcome measures were reduction in headache duration and severity. In addition, we studied the effect of these medications on headache disability score using the Paediatric Migraine Disability Assessment (PedMIDAS) questionnaire, as well as their adverse side effects. The trial was continued for three months after administering the medications. Results: We enrolled 66 children with migraine, and 60 of them completed the study (30 in each arm). Ninety per cent (27/30) of children in each arm showed more than 50% reduction in monthly headache frequency. Duration and severity of headaches were also significantly decreased at the end of the trial. In addition, the safety profile of medications was acceptable, and headache disability score was significantly improved at the end of the trial. Conclusions: These results indicate that levetiracetam might be effective and safe in the prophylaxis of migraine headaches in children. It deserves to be considered in the prophylaxis of migraine headaches in children.