Objective: The aim of this study was to investigate and analyze the prognostic factors affecting lymph node (LN) metastasis and postoperative recurrence in patients with primary small cell carcinoma of the esophagus (SCCE). Methods: A total of 125 primary SCCE patients who received surgical resection in the Fourth Hospital of Hebei Medical University between March 2005 and August 2009 were included in this retrospective study. All the potential prognostic variables, including the patients' characteristics, tumor features, and treatment modalities, were analyzed by a Cox regression model to explore LN metastasis and the factors associated with postoperative recurrence. Results: LN metastasis rate was significantly correlated with depth of tumor invasion (p < 0.001) and tumor length (p = 0.006). LN metastasis ratio was positively correlated with pathological type (p < 0.001), tumor location (p = 0.002), depth of tumor invasion (p < 0.001), and tumor length (p < 0.001). LN stage and chemotherapy were found to be the independent risk factors for progression-free survival (PFS). Conclusion: Depth of tumor invasion and tumor length were main factors associated with LN metastasis in primary SCCE. The stage of LN metastasis and chemotherapy was independent factors affecting the postoperative PFS.