Background As a subtype of esophageal neuroendocrine neoplasms (ENENs), esophageal neuroendocrine carcinoma (ENEC) is rare. ENEC can be poorly differentiated and highly aggressive. This study aims to illustrate the incidence, treatment, and prognosis of ENEC by using a population-based database. Methods We collected clinicopathological data [1975–2016] of ENEC, esophageal adenocarcinoma (EACA), and esophageal squamous cell carcinoma (ESqCC) from the Surveillance, Epidemiology and End Results (SEER) database, and analyzed their incidence, treatment, and prognosis. Results A total of 60,238 cases were in our study cohort, including ENEC (n=686), EACA (n=26,575), and ESqCC (n=32,977). The incidence of ENEC in 2016 was 0.044 per 100,000 persons. The tumor grade of ENEC was significantly higher than that of EACA and ESqCC (P<0.001). Both cancer-specific survival (CSS) and overall survival (OS) of ENEC were significantly worse than those of EACA and ESqCC (P<0.001). Kaplan-Meier analysis showed significant improvement of CSS and OS by surgery, radiotherapy, and chemotherapy (all P<0.001). Besides, compared with monotherapies, combinational therapies brought more benefits to both CSS and OS of patients with ENEC. Conclusions Our population-based evidence revealed that ENEC, as a rare cancer, had a worse prognosis, compared with EACA and ESqCC. Surgery, chemotherapy, and radiotherapy can all improve the prognosis of ENEC patients. Combinational therapy can yield a better prognosis than monotherapy.