Headache and allergic rhinitis (AR) are common in children and often co-occur. We investigated the clinical characteristics of pediatric headaches and the association of AR and chronic headaches. We retrospectively reviewed the medical records of patients admitted to our pediatric inpatient and outpatient clinics with complaints of headache between January 2017 and June 2020 for headache-specific history, AR signs and symptoms, allergy skin prick test, inhalant multiple allergen simultaneous test results, laboratory and imaging findings, and medication history. The patients were divided into three subgroups: AR, non-AR, and headache groups, reporting 45.7% patients with headache alone, 13.7% with additional AR, and 31.6% with abnormal imaging findings, suggesting that headache was combined with sinusitis (24.3%) or mastoiditis (7.3%). Furthermore, 6% of the patients had both AR and sinusitis. Body mass index (BMI) differed significantly between the AR and the non-AR and headache groups (p = 0.03). The BMI differed significantly according to headache severity (p ˂ 0.001). The most common allergen was “dust or mites” (41.1%). Acetaminophen (35.9%) was the most commonly used painkiller. The coexistence of AR and headache may indicate that these conditions share a similar pathophysiology. Better management of allergies may facilitate diagnosis, treatment, and prophylaxis of headaches.