Background: The aims of this study were to investigate the prevalence of allergic rhinitis (AR) and the accuracy of the International Study of Asthma and Allergies in Childhood (ISAAC) questions for diagnosis of AR, in Korean children. Methods: Students that participated in an allergic disease prevalence survey in 2010–2017 were evaluated (n = 18,425) using questionnaires and a skin prick test (SPT). Age−stratified (5−7, 8−10, 11−13, 14−16 years) prevalence of four rhinitis questions, accuracy of the questions for AR, and proportion of comorbidities in the AR and non-AR (NAR) groups were evaluated. Results: The proportion of students responding to the questionnaire that ever had symptoms of AR since birth, that is, the prevalence of “symptom, ever” was 47.6%. Based on the questionnaire and SPT, overall prevalence of AR and NAR were 21% and 26.5%, respectively. The sensitivity, specificity, and accuracy of “symptom, ever” were 57.5%, 58.4%, and 58.1%, respectively, and those of “diagnosis, ever”, who had ever been diagnosed with AR, were 39.8%, 76.9%, and 63.4%, respectively. Questionnaire−based asthma, atopic dermatitis, and food allergy were significantly associated with the AR group compared to the NAR group. Conclusions: Since the AR accuracy of the questionnaire is about 60%, it should be considered that the questionnaire based survey overestimates the true prevalence of AR in Korean children.