Background Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract, with rectal involvement being relatively rare, accounting for approximately 5% of all GISTs. Due to the unique anatomy of the rectum, most rectal GISTs originate from the muscularis propria, which increases the risk of perforation during endoscopic resection. Although traditional surgical resection offers a high rate of complete removal, it is often associated with greater trauma and insufficient functional preservation. With advances in endoscopic techniques, endoscopic submucosal excavation (ESE) has been increasingly used in the management of small rectal GISTs; however, successful preservation of the rectal serosal layer during ESE remains rarely reported.Case Presentation A 51-year-old woman was found to have a 0.5 cm submucosal lesion located 12 cm from the anal verge during a screening colonoscopy. Endoscopic ultrasonography (EUS) revealed a heterogeneous hypoechoic lesion arising from the muscularis propria (4.7 & times; 4.0 mm). Contrast-enhanced MRI suggested a neuroendocrine tumor. After exclusion of contraindications, ESE was performed, achieving complete tumor removal with negative margins. Notably, the serosal layer of the rectal wall was fully preserved, preventing perforation. The mucosal defect was prophylactically closed with endoscopic clips. Postoperative recovery was uneventful, and no complications occurred.Conclusion ESE can achieve complete resection of small rectal GISTs while preserving the serosal layer and rectal function. Although this case demonstrates the feasibility and safety of serosal-sparing ESE, further studies with larger sample sizes and long-term follow-up are warranted.