This study aimed to compare the tumor characteristics and long-term outcomes between EGIST and GIST. The confounding function was applied to improve the result credibility in the case of small sample size. Design, Setting, and Participants. This cohort study enrolled 55 patients with EGIST who underwent surgery and were selected from four high-volume hospitals in China and 221 GIST patients who were collected from one of the four hospitals between January 2006 and September 2017. We used propensity score matching (PSM) and subgroup analysis to compare EGIST with GIST in terms of prognosis. The confounding function was used for sensitivity analysis to reduce unmeasured confounding.We matched 43 patients in each of the GIST and EGIST groups by PSM. We compared EGIST data with GIST data to explore the prognostic factors between them. In the multivariate Cox regression model, tumor location of EGIST was negatively correlated with overall survival (after PSM: HR, 4.32; 95% CI, 1.22-15.26) or disease-free survival (after PSM: HR, 9.79; 95% CI, 2.22-43.31), which was also intuitively shown in the Kaplan-Meier survival curves (all P values < 0.05). In the subgroup analysis, EGIST with high risk factors had a worse prognosis than GIST. In unmeasured confounding analysis, the overall curve tends to show all combinations of c(0) of c(1) up to 2.0, none of which would bring the corrected relative risk to 1 for OS and DFS. Conclusions and Relevance. EGIST was associated with worse prognosis compared with GIST patients, particularly in EGIST patients with high risk factors, while there was a similar prognosis without those high risk factors.Copyright © 2021 Huolun Feng et al.