Migraine is a common condition in the pediatric population and causes a significant impact on the quality of life. Atopic disorders are some of the migraine comorbidities. Objective We hypothesized that allergic rhinitis could aggravate migraine in the pediatric population. Methods This cross-sectional study consecutively evaluated 90 pediatric outpatients (46 children 6–12 years of age; 44 adolescents up to 18 years of age) who sought medical assistance because of migraine at a general neurology clinic in Passo Fundo, RS, Brazil. They, and their parents, were given three questionnaires, to evaluate the diagnosis of current allergic rhinitis, allergic rhinoconjunctivitis and seasonal allergic rhinitis, as well as the disability caused by headache (ISAAC - International Study of Asthma and Allergies in Childhood; CARATkids - Control of Allergic Rhinitis and Asthma Test for Children; PedMIDAS - Pediatric Migraine Disability Assessment). The study was approved by the local ethics committee. Results According to the ISAAC questionnaire, children with current allergic rhinoconjunctivitis in the last year showed higher scores on the PedMIDAS than those patients without atopy (median and interquartile range 26 [10–58] vs. 5 [1–13], p = 0.008). A significant positive correlation of CARATkids scores with PedMIDAS scores was found (p = 0.007, rho = 0.39). After including other putative predictors of migraine disability (age, body mass index, time since onset of migraine) in a multiple regression analysis, only the scores on the CARATkids remained a significant independent variable correlated with PedMIDAS scores (p = 0.001; R = 0.55; R2 = 0.30). Conclusions Current allergic rhinoconjunctivitis is related to enhanced disability caused by headache in childhood migraine.