Introduction: Migraine is a common pediatric neurological disorder, and its relationship with allergic disease in early childhood remains incompletely defined. Objective: To explore the prevalence and distribution of allergic disorders among children with migraine. Methods: The electronic medical records from a large Health Maintenance Organization were searched, spanning from 2000 to 2023, for children from birth to 5 years of age diagnosed with allergic diseases who were diagnosed with migraine at age 5-18 years. Demographic characteristics and allergic comorbidities were analyzed and compared between children with migraine with and without allergic disease. Results: Among 6,839 children with migraine, 2,216 (32.4%) had at least one allergic comorbidity. Children with allergic disease presented at a younger age than those without allergies (median age 3 vs. 4 years, p < 0.001). Asthma was the only allergic disease that demonstrated a significant sex difference, being more common in males (p = 0.011). High socioeconomic status was the most common category in most allergic diseases, except for asthma. Atopic dermatitis was the most common allergic condition (41.7%), and multimorbidity was uncommon. Conclusions: This study demonstrates that allergic diseases in early childhood are associated with younger age at migraine diagnosis and with distinct demographic patterns. The distribution of allergic phenotypes in early-life observed in the cohort may play a role in migraine susceptibility. Future research should explore the mechanistic pathways linking early-childhood atopy and migraine and evaluate whether targeted management of allergic diseases can modify migraine outcomes in children.