Background: The main purpose of this study is to analyze the clinicopathological features and prognosis factors of bile duct and ampullary neuroendocrine neoplasms (NENs). Methods: The relevant data were collected from the SEER database from 1975 to 2016. The Kaplan–Meier curve and Cox model were used for survival analysis. The nomogram was drawn to predict the survival rate. The calibration, discrimination and clinical utility of the nomogram were evaluated by calibration curve, the concordance index (C-index) and decision curve analysis (DCA). Results: A total of 340 cases were included in our research. According to Kaplan–Meier analysis, 1-year, 3-year and 5-year of overall survival (OS) were 77.3%, 61.9% and 58.4%, while 1-year, 3-year and 5-year of the disease-specific survival (DSS) were 82.7%, 69.3% and 66.9%, respectively. The multivariable analysis results showed that age, histological grade, SEER stage and surgery were independent predictors for either OS or DSS. The calibration curve and the C-index value indicated that the nomogram was well calibrated and had good discrimination. DCA showed that the model had ideal net benefits. Conclusions: The age, histological grade, SEER stage and surgery were identified as independent prognostic variables for OS and DSS. After verification, nomogram has good predictive ability and clinical application value.