Purpose To explore differences in long-term outcomes between gastric neuroendocrine carcinoma (GNEC) and gastric adenocarcinoma (GAC). Methods One hundred GNEC patients and 3089 GAC patients were enrolled. Differences in long-term outcomes between the groups were analyzed by 1:2 propensity score matching. Results Statistically significant differences between the groups were noted in terms of gender, American Society of Anesthesiologists score, tumor size, T stage, N stage, TNM stage and surgical approach. However, differences were not significant after matching. The 3-year and 5-year overall survival rates for the GNEC group were reduced compared with those for the GAC group, though disease-free survival rates and mean recurrence times were similar. Notably, the mean post-recurrence survival of the GNEC group was significantly worse than that of the GAC group (5.2 vs. 14.8 months, p<0.001). A strong negative correlation was found between a high Ki-67 labeling index and overall survival time. Cox regression analysis indicated the Ki-67 labeling index to be an independent factor influencing patient post-recurrence survival. Conclusions The long-term oncologic outcome of GNEC was worse than that of GAC, which may be relative to its reduced post-recurrence survival. A high Ki-67 labeling index was an independent factor influencing patient post-recurrence survival.