Objective: It is vital to detect life-threatening conditions in patients presenting to the pediatric emergency department with symptoms of headache. In this study, we aimed to evaluate patients who presented to our pediatric emergency department with symptoms of headache, and to determine which findings deserved the most attention in the anamnesis and during physical examinations. Methods: Patients who presented to the pediatric emergency department with symptoms of headache between July 2018 and June 2019 in Ankara, Turkey, were evaluated, retrospectively. Results: During the study period, 743 patients were included in the study. The median (IQR) age was 160.0 (range, 20.0-192.0) months. The male and female distribution was 46.2% (n = 343) and 53.8% (n = 400), respectively. The most common cause of headache was upper respiratory tract infections (84.2%). Severe headache symptoms were present in 2.3% of the entire patient group. In 81.2% of the patients with severe headache, various pathologic neurologic findings such as diffuse headache, nocturnal awakenings, vomiting, visual disturbances, nystagmus, cranial nerve pathologies, weakness, altered mental status, speech difficulty, and meningismus were present. Seventy-nine (10.6%) patients underwent neurologic imaging, and 15 (19.0%) had pathologic findings. Conclusion: Our data support that the most common cause of headaches in the pediatric emergency department is upper respiratory tract infections. The coexistence of nocturnal awakenings and/or the presence of pathologic-neurologic findings are red flags for cases of severe headache.