Current clinical practice suggests lymphadenectomy for gastrointestinal stromal tumor (GIST) patients with enlarged lymph nodes, but little is known about the influence of lymphadenectomy on long-term survival.This population-based study consisted of 3,819 non-metastatic GIST patients diagnosed between January 1, 2001, to December 31, 2015, from the Surveillance, Epidemiology, and End Results (SEER) database. Kaplan-Meier methods and Cox proportion regression models were used to compare differences in overall survival (OS) and cancer-specific survival (CSS) between the lymphadenectomy group and non-lymphadenectomy group.Among the 3,819 GIST patients, 1,202 received lymphadenectomy and 2,617 did not receive lymphadenectomy. Lymphadenectomy was associated with poor OS (adjusted HR =1.25, 95% CI: 1.06-1.47) and CSS (adjusted HR =1.32, 95% CI: 1.07-1.64) in GIST patients. This was especially evident in GIST patients with a tumor size less than 2 cm (OS, HR =1.91, 95% CI: 0.79-4.60 and CSS, HR =6.37, 95% CI: 1.85-21.90), who were more than 40 years old (OS, HR =1.28, 95% CI: 1.08-1.51 and CSS, HR =1.36, 95% CI: 1.09-1.70), and with a stomach tumor (OS, HR =1.39, 95% CI: 1.12-1.72 and CSS, HR =1.77, 95% CI: 1.33-2.35).In conclusion, contrary to what was previously presumed, lymphadenectomy was associated with an increased and not a decreased risk of mortality in GIST patients.