Objective: Laparoscopic resection is increasingly performed for gastrointestinal stromal tumors (GISTs). However, the laparoscopic approach for GISTs located in the esophagogastric junction (EGJ-GIST) is surgically challenging. This study compares the efficacy of laparoscopic surgery and the open procedure for EGJ-GIST through the propensity score weighting (PSW) method. Methods: Between April 2006 and April 2018, 1,824 surgical patients were diagnosed with primary gastric GIST at four medical centers in South China. Of these patients, 228 were identified as EGJ-GISTs and retrospectively reviewed clinicopathological characteristics, operative information, and long-term outcomes. PSW was used to create the balanced cohorts. Results: PSW was carried out in laparoscopic and open-surgery cohorts according to year of surgery, sex, age, body mass index (BMI), tumor size, mitotic rates and recurrence risk. After PSW, 438 patients consisting of 213 laparoscopic (L group) and 225 open surgery (0 group) patients were enrolled. After PSW, the following measures in the L group were superior to those in the 0 group: median operative time [interquartile range (IQR)] : 100.0 (64.5-141.5) vs. 149.0 (104.0-197.5) min, P<0.001; median blood loss (IQR): 30.0 (10.0-50.0) vs. 50.0 (20.0-100.0) mL, P=0.002; median time to liquid intake (IQR): 3.0 (2.0-4.0) vs. 4.0 (3.0-5.0) d, P<0.001; median hospital stay (IQR): 6.0 (4.0-8.0) vs. 7.0 (5.0-12.0) d, P<0.001; and postoperative complications (10.3% vs. 22.7%, P=0.001). The median follow-up was 55 (range, 2-153) months in the entire cohort. No significant differences were detected in either relapse-free survival (RFS) [hazard ratio (HR): 0.372, 95% confidence interval (95% CI): 0.072-1.910, P=0.236) or overall survival (OS) (HR: 0.400, 95% CI: 0.119-1.343, P=0.138) between the two groups. Conclusions: Laparoscopic surgery for EGJ-GIST is associated with the advantages of shorter operative time, reduced blood loss, shorter time to liquid intake, and shorter length of stay, all without compromising postoperative outcomes and long-term survival.