Introduction: Epilepsy and migraines are frequently observed as comorbidities, with the occurrence of one disorder increasing the probability of the other. The aim of our study was to evaluate the EEG characteristics by the type of headache and the implications of EEGs in headache patients, comparing the clinical characteristics and treatments between the headache patients with normal and abnormal EEGs. Methods: We conducted a retrospective analysis reviewing the medical records of 259 patients with headaches who visited the pediatrics departments of five university hospitals and underwent EEGs over a period of 3 years. Based on the data entered, analyses of the following items were conducted: (1) comparison of the EEG abnormalities by the type of headache and the characteristics of the EEG findings and (2) comparison of the clinical characteristics between patients with normal and abnormal EEGs. Results: Of the 259 patients, 31 showed abnormal EEGs, while 228 had normal EEGs. Of the 31 patients with abnormal EEGs, 17 showed epileptiform discharges, and 11 showed rhythmic slowing. The frequency of EEG abnormalities was significantly high in patients with migraines with auras than other types of headache. The Pediatric Migraine Disability Assessment (PedMIDAS) score was significantly higher in the abnormal EEG group compared with the normal EEG group (p = 0.001). Conclusion: The results of this study suggest that the abnormal EEG group had more significant disruptions in their daily lives due to headaches than the normal EEG group and that patients with migraines with aura may need EEGs and they might also have overlapping pathophysiologic mechanisms with epilepsy.