Introduction Headache is a frequent complaint in children and adolescents. Decision-making for neuroimaging should take into account the cost and the need for sedation in young children. Aim To evaluate the yield of MRI in pediatric headache patients seen in two large tertiary hospitals. Methods Data were retrospectively collected from patient records (n = 613) and neuroimaging reports. Headache was classified according to International Headache Society guidelines. Results There were 346 children with imaging studies (MRI n = 281, CT n = 65). Of patients who had at least one MRI study, 29% demonstrated an abnormal finding. Findings altering the management were obtained in 21 (7%) patients: the majority (n = 17, 80%) had headache for less than 3 months. On the other hand, four patients with headache longer than 3 months (19%) and 12 patients with normal neurological examination (57%) had significant MRI results affecting management. None of the children in whom the diagnosis of migraine could be made on clinical grounds (n = 40) had a significant MRI finding. Conclusion Neuroimaging should be performed selectively in children with headache seen in pediatric neurology clinics, especially in headache of short duration (< 3 months) and features atypical for migraine. A normal neurological examination should not reassure the clinician.