Introduction Sleep-disordered breathing (SDB) in primary school children is a significant problem, yet its prevalence is not well known outside large urban settings. Information on the burden and risk factors of SDB in children could be used to improve resource allocation when providing care across a large country. The objectives of this study were to assess the prevalence of SDB among school-aged children comparing rural and urban settings, and to investigate associated risk factors. Methods In this cross-sectional study, a random sample of primary school students in Turkey were selected from urban and rural areas and data were collected using the Pediatric Sleep Questionnaire, asthma, and allergic rhinitis questionnaires completed by the parents. Results Questionnaires were collected from a total of 139 schools from 58 provinces. A total of 11,013 students were contacted, and 9045 (73%) completed the study. There was no difference in the prevalence of SDB between rural and urban settings (16% vs. 15%,p = 0.612). Multivariate logistic regression analysis revealed that current wheezing, current rhinoconjunctivitis, being overweight, parental snoring, and current mold at home were significant risk factors for SDB in both rural and urban children. Current tobacco smoke exposure (OR = 1.48, 95%CI = 1.19-1.85), near roadway air pollution exposure (OR = 1.40, 95%CI = 1.108-1.791), and mold at home in the first year of life (OR = 1.68, 95%CI = 1.26-2.23) were associated with SDB in urban children. History of maternal/paternal adenotonsillectomy was a significant predictor of SDB in the rural setting (OR = 1.63, 95%CI = 1.12-2.39). Conclusion The prevalence of SDB is high in children living in both settings but associated risk factors may vary. Children residing in rural areas should also be screened for sleep-disordered breathing during routine health visits.