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Neuroendocrine tumors of the thymus (NETTs) are rare but aggressive, and lead to poor overall survival. This retrospective study was designed to analyze factors that correlate with the prognosis of patients with NETTs.From 1999 to 2015, 41 ongoing patients with NETTs were enrolled in this study. The clinical data and outcome were compiled. Overall survival (OS) rate was analyzed using the Kaplan–Meier method in univariate analysis and the Cox-model was used in multivariate analysis.Of the 41 NETTs patients analyzed (31 male and 10 female), 12 were typical carcinoma, 14 were atypical carcinoma, 14 were small-cell carcinoma and, 1 was large-cell carcinoma. The median follow-up time was 29 months (range, 9.0–69.0). In total, 25 patients died of cancer-related disease by the last follow-up. The 3- and 5-year survival rates for all patients were 42.7% and 23.4%, respectively. Among the prognostic factors analyzed by multivariate analysis, low tumor grade, complete resection, and a negative chromogranin A (CgA) expression were positively correlated with survival.The surgical treatment of NETTs, CgA negative, and low grade of NETTs were associated with a statistically significant better prognosis. However, large, multicenter studies are required to fully validate these prognostic factors.