This study evaluates specific electroencephalogram abnormalities in pediatric migraine and tension-type headaches, and demonstrates the clinical value of these abnormalities. We studied 50 migraine patients and 50 tension-type headache patients. Their mean age ± SD was 10.62 ± 3.21 (range, 5-16) years in the migraine group, and 13.00 ± 2.37 (7-16) years in the tension-type headache group. Diagnoses were rendered according to the International Classification of Headache Disorders, 2nd Edition, First Revision, of the International Headache Society. All patients underwent two waking-state electroencephalograms, one during a headache, and the other when headache-free. Thirty-six percent (18/50) of migraine patients and 12% (6/50) of tension-type headache patients revealed specific electroencephalogram abnormalities in headache attack electroencephalograms (P < 0.05). In headache-free period electroencephalograms, 16% (8/50) of the migraine group and 2% (1/50) of the tension-type headache group revealed abnormalities (P < 0.05). Our results indicate that electroencephalogram abnormalities are particularly prevalent in migraines, especially during headache attacks. This study is the first, to the best of our knowledge, on electroencephalographic evaluation of pediatric migraine and tension-type headache patients during both headache attacks and headache-free periods.