Abstract Background and study aims Histological confirmation of subepithelial lesions (SELs) in the upper gastrointestinal tract remains challenging. Endoscopic resection of SELs is increasingly used for its excellent diagnostic yield and opportunity to do away with continued surveillance. In this study, we aimed to evaluate the indications, success rates and complications of different endoscopic resection techniques for SELs at a large, tertiary referral hospital in Rotterdam, The Netherlands. Patients and methods Data between October 2013 and December 2021 were retrospectively collected and analyzed. Main outcomes were R0-resection rate, en bloc resection rate, recurrence rate, and procedure-related adverse events (AEs) (Clavien-Dindo). Secondary outcomes were procedure time, need for surgical intervention, and clinical impact on patient management. Results A total of 58 patients were referred for endoscopic resection of upper gastrointestinal SELs. The median diameter of lesions was 20 mm (range 7–100 mm). Median follow-up time was 5 months (range 0.4–75.7). Forty-eight procedures (83%) were completed successfully leading to en bloc resection in 85% and R0-resection in 63%. Procedure-related AEs occurred in six patients (13%). Severe complications (CD grade 3a) were seen in three patients. The local recurrence rate for (pre)malignant diagnosis was 2%. Additional surgical intervention was needed in seven patients (15%). A total of 32 patients (67%) could be discharged from further surveillance after endoscopic resection. Conclusions Endoscopic resection is a safe and effective treatment for SELs and offers valuable information about undetermined SELs for which repeated sampling attempts have failed to provide adequate tissue for diagnosis.