There is currently no universally accepted staging system for esophageal neuroendocrine neoplasms (ENENs). In the present study, patients with ENENs, identified from the Surveillance, Epidemiology, and End Results registry (SEER) (n=191 patients) and the multicentric series (n=51 patients), were stratified to assess the validity of the 8th American Joint Committee on Cancer (AJCC) staging systems, particularly for esophageal squamous cell carcinoma and esophageal adenocarcinoma. The Kaplan-Meier method was used to assess disease-specific survival (DSS), according to the Tumor-Node-Metastasis (TNM) status, and the Cox model was applied to evaluate differences in prognosis after adjustment for potential confounders. For the 8th AJCC staging classifications, only the pathological stage groups (pTNM) conferred increased hazard ratios from stage I to stage IV, with overlaps between adjacent stages. According to the current findings, the regional lymph nodes involvement status other than the current N classification was a significant predictor of DSS. Consequently, a revised N(Nr) classification was proposed and therefore a new TNrM staging system was adopted, for which progressively poorer DSS associated with increasing stage was observed. Moreover, the concordance index with the modified staging system was slightly higher in patients with ENENs from the SEER registry compared with that of the 8th pTNM system. In conclusion, lymph node status, rather than the number of positive lymph nodes, was a marker of poorer DSS and the modified staging system provided an easier and more accurate staging tool. The present results indicate that revisions to the current staging classifications may be improve the assessment of patient prognosis.