The prognostic importance of the neuroendocrine (NE) markers involving neural cell adhesion molecule (NCAM) has been unclear enough to be adopted for WHO classification in patients with pancreatic neuroendocrine neoplasms (Pan-NENs). This study aimed to elucidate whether the three NE markers such as chromogranin A, synaptophysin, and NCAM decide prognoses for patients with well-differentiated tumors.Between April 2002 and October 2018, 217 patients were included in this study. Tissue samples from tumors of Pan-NENs were immunochemically stained for the aforementioned NE markers. Diffuse and intense staining was defined as positive, while faint or focal staining and non-staining were considered negative.The median age of patients was 55 years. The median observation period was 1415 days. In multivariate analysis of progression-free survival (PFS), liver metastasis, Ki-67 index, and triple-positive staining of NE markers were risk factors. The 5-year PFS rate of patients with and without triple-positive NE markers was 56.3% and 23.8%, respectively (P < 0.0001). In multivariate analysis of overall survival (OS), R0 resection, Ki-67 index and triple-positive NE markers (hazard ratio 0.4, P = 0.02) were the risk factors. The 5-year OS rate of patients with and without triple-positive NE markers was 88.8% and 66.4%, respectively (P = 0.014). The tumors of patients without triple-positive NE markers were associated with large tumor size, a high mitotic rate and high Ki-67 index.Triple-positive NE marker staining was a simple and practical indicator of prognoses in patients with well-differentiated Pan-NETs.