This study aims to compare the clinical outcomes of endoscopic and open approaches in patients with gastrointestinal stromal tumor (GIST). GIST is a relatively rare type of neoplasms. It represents 1% of gastrointestinal tumors (GITs) and 20-30% of all malignancies. Most of the GISTs develop in the area of stomach. In this retrospective study, 77 patients who underwent surgery for GIST tumors within length of 1.5-4 cm were divided into two groups according to type of surgical approach: open surgery (OS group, n=36) and endoscopy resection (ER group, n= 41). The clinical outcomes were compared between the two groups. OS group contains 36 in total with 58.33% male and 41.67% female. ER group contains 41 in total with 43.9% male and 56.1% female. In comparison to conventional OS, patients treated with endoscopic ultrasonography (EUS) guided ER showed significantly less time in surgery procedure, less operative blood loss, less complication rates, less duration for postoperative fasting and postoperative hospitalization, indicating a quicker recovery and better clinical outcome. Furthermore, treatment group with ER displayed reduced expense of hospitalization due to lower procedure expense and shorter hospital stay with rare tumor recurrence. Here, we also included an example case report of successful treatment of GIST with ER. Endoscopic tumor resection is an effective method to remove non-high risk GISTs in patients comparing to OS, and may be beneficial to patients economically.