NKX6-1 is a homeobox transcription factor participating in the development and regulation of endocrine function of pancreatic islets. This study evaluated the potential use of NKX6-1 as a diagnostic marker for well-differentiated neuroendocrine tumors (WDNETs). In total, 178 primary and 26 metastatic WDNETs of different origins were analyzed through immunohistochemistry for NKX6-1, TTF-1, CDX2, ISL1, and polyclonal PAX8. NKX6-1 was expressed in 36 of the 44 (82%) primary pancreatic WDNETs, 12 of the 18 (67%) primary duodenal WDNETs, and rarely in pulmonary, gastric, and appendiceal WDNETs. The specificity of using NKX6-1 as a marker for pancreatic and duodenal WDNETs is 93%. Of the 26 metastatic WDNETs, NKX6-1 was expressed only in the tumors of pancreatic origin (sensitivity: 63%, specificity: 100%). The combinatorial use of NKX6-1, CDX2, TTF-1, and ISL1 distinguished WDNETs of different origins with high specificity. Our results indicated that the inclusion of NKX6-1 in an immunohistochemical panel will be beneficial for identifying the primary sites of WDNETs.