Background Organ preservation protocols have increasingly been applied for the treatment of head and neck cancers, including hypopharyngeal squamous cell carcinoma (HSCC). We sought to evaluate whether patients treated with primary surgery followed by adjuvant therapy had survival benefit over patients treated with initial nonsurgical modalities. Methods We retrospectively reviewed patients with new diagnosis of HSCC at the University of Pittsburgh (1994‐2014) treated with either primary total laryngectomy with pharyngectomy or organ preservation. Results One hundred thirty‐seven patients were identified. Surgical cases were more likely to be of advanced T stage. Initial surgery was more likely to be performed in the earlier years of the cohort. After adjusting for this imbalance using a propensity score, primary surgery was associated with improved survival compared with nonoperative therapy (P = 0.02). Conclusions Due to its survival advantage, primary surgery followed by adjuvant treatment should be considered as a viable treatment of HSCC.