Background: There is ongoing debate about surgery of primary site in nasopharyngeal carcinoma patients. Methods: 3919 patients with nasopharyngeal carcinoma identified in the SEER registry between 2004 and 2013. The benefit of surgery of primary nasopharynx tumor site on overall and cancer-specific survival was assessed by risk-adjusted multivariate Cox proportional hazard regression and propensity score matching modeling. Results: Surgery was marginally associated with better overall survival (hazard ratio (HR) = 0.816, 95% CI 0.656-1.015, p = 0.07) and cancer-specific survival (HR = 0.749, 95% CI 0.552-1.018, p = 0.06) in the propensity score model. Among 398 cases who underwent primary site surgery, 282 (70.85%) received local tumor excision and 79 (20.31%) received pharyngectomy. Local tumor excision and pharyngectomy had almost the same effect on survival in propensity score matching analysis. The benefit was significant in subgroups of white, age < 60 year, and patients with T3, N1, M0, AJCC stage III, or moderately differentiated tumors. Further survival analysis showed surgery to promote survival in both radiotherapy and non-radiotherapy patients. Conclusion: This is the first population-based analysis using propensity score model to provide evidence of a positive impact of surgery on survival in nasopharyngeal carcinoma. Moreover, surgery demonstrated the significant benefit in subgroups of patients with specific clinical characteristics.