Background and aimsWith the development of endoscopic technology, endoscopic treatment has been widely used in Gastrointestinal stromal tumors (GISTs). However, population-based studies comparing the long-term results of patients who received endoscopic treatment vs. Surgery are lacking. We used the Surveillance, Epidemiology, and End Results (SEER) database to analyze the long-term survival of colorectal or gastric GISTs who underwent primary tumor resection (endoscopic therapy or surgery) in the USA. Methods Patients with colorectal or gastric GISTs were selected from the SEER database between 2010 and 2015. Kaplan-Meier analyses and log-rank tests were used to evaluate the difference in the long-term survival between the endoscopic therapy group and the surgery group. We examined the association between different treatments and survival after using the multivariate cox proportional hazards model to adjust the relevant covariates. Besides, we used Propensity score matching (PSM) to overcome the different distributions of covariates between the two groups and then further compare the survival difference. Results In total, 2355 patients were enrolled in our study, of which 1999 (84.9%) received surgical treatment and 356 (15.1%) received endoscopic treatment. There was no significant difference in overall survival (OS) between the two groups before PSM. The median OS (73.5 months vs. 72.2 months) and 5-year OS rate (85.7% vs. 81.5%) of endoscopic therapy were similar to surgical patients (P = 0.34). The median Cancer-specific survival (CSS) and 5-year CSS rate in the endoscopic treatment group were higher than the surgical group before PSM, with 81.3 months, 97.1% versus 78.8 months, 92.7% (P = 0.011). After adjusting for other clinical factors and PSM, the long-term OS and CSS did not significantly differ between those treated surgically and treated endoscopically. Conclusion Based on the American population, we preliminarily found that the long-term OS and CSS did not differ between patients undergoing endoscopic therapy and surgery.