BACKGROUND: Rectal schwannoma (RS) is a rare subtype of schwannoma that presents diagnostic challenges owing to its clinical rarity. The absence of typical symptoms, specific signs, and distinctive radiographic findings often hinders clinicians from reaching a definitive diagnosis before surgical intervention. Herein, we report a case of RS who underwent complete resection through endoscopic full-thickness resection (EFTR) and discuss the clinical, imaging, and pathological features for differential diagnosis. CASE SUMMARY: A 71-year-old Chinese woman presented to our outpatient clinic with a 4-year history of a rectal mucosal mass for a follow-up surveillance colonoscopy. A neurogenic tumor with extraluminal growth was considered based on the imaging findings. Resection was required, and an EFTR was performed. On endoscopic exploration, a smooth surface extruding mass was identified at the rectum. The patient was discharged 48 hours after the operation without infection or bleeding. Based on the pathological and immunohistochemical findings of the resected mass, a rectal benign schwannoma was diagnosed. The patient did not undergo any adjuvant therapy. Nearly one year later, a follow-up surveillance colonoscopy and an abdominal and pelvic plain plus enhancement scan were performed, and no tumor recurrence or metastasis was noted. CONCLUSION: EFTR is safe and effective for resecting gastrointestinal stromal tumors, especially those with extraluminal growth and no lymph node involvement.