The association between migraine and allergy has remained a subject of debate for more than a century. To systemically investigate the interaction between children with antecedent allergic diseases and their future risks of migraine on reaching school age, we recruited 16,130 children aged 7–18 with migraine diagnosed between 2000 and 2008, and 64,520 matched controls without a history of migraine. The ORs of migraine were calculated for the association with allergic diseases diagnosed before migraine diagnosis. The allergic diseases included atopic dermatitis, allergic conjunctivitis, allergic rhinitis (AR), and asthma. Children with preceding allergic diseases had a greater subsequent risk of migraine than the controls. Among the four evaluated diseases, AR had the highest adjusted OR (aOR) of 2.17 (95% CI 2.09 to 2.26). Children with all four allergic diseases had the highest aOR of 3.59 (95% CI 2.91 to 4.44). Further, an increasing trend of aORs was observed with more allergic disease-associated medical consulting. Our study indicates that children with allergic diseases are at increased subsequent risk of migraine when they reach school age, and the risk shows a cumulative effect of more allergic diseases and more allergy-related healthcare.