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Background Head and neck cancer is increasingly being managed through nonsurgical approaches. Evidence comes from studies that have mainly examined patients with laryngeal cancer. Few studies, with limited sample size, have focused on the comparative outcomes of surgical and nonsurgical approaches in patients with advanced oropharyngeal or hypopharyngeal cancer. Methods Using a national cancer database, we identified 1603 and 1512 patients with clinical stage III/IVA oropharyngeal and hypopharyngeal cancer, respectively, treated between 2004 and 2009. The study cohort was followed until 2012, and analyzed through Kaplan-Meier survival analysis and Cox regression. Results Overall, 31.4% of patients with advanced oropharyngeal cancer and 42.2% of patients with hypopharyngeal cancer received surgery as their primary treatment. Receiving primary surgery for advanced oropharyngeal and hypopharyngeal cancer was associated with higher survival rates after controlling for potential confounders. Conclusion We recommend that surgery be considered a first-line treatment for advanced oropharyngeal and hypopharyngeal cancers.