Abstract: Rectal subepithelial lesions (SELs) are commonly seen in endoscopic examination, generally manifested as bumps with a smooth surface. Precise preoperative diagnoses for rectal SELs are difficult because abnormal tissues are not easily to be obtained by regular endoscopic forceps biopsy. Traditional guidance modalities of preoperative biopsy, including endoscopic ultrasound, computed tomography, and transabdominal ultrasound, are often unsatisfactory. An updated, safe, and effective biopsy guidance method is required. We herein report a new biopsy guidance modality—endorectal ultrasound (ERUS) combined with contrast-enhanced ultrasound (CEUS). A 32-year-old woman complained of a mass inside the rectovaginal space for 9 years, which became enlarged within 1 year. A rectal SEL detected by endoscopy was suspected to be a gastrointestinal stromal tumor or exophytic uterine fibroid. Pathological diagnosis was difficult because of unsuccessful transabdominal core needle biopsy with insufficient tissues, as well as vaginal hemorrhage. A second biopsy was suggested after multiple disciplinary treatment discussion, which referred to a transperineal core needle biopsy (CNB) guided by ERUS combined with CEUS. Adequate samples were procured and rectal gastrointestinal stromal tumor was proved to be the pathological diagnosis. Imatinib was recommended for first-line therapy by multiple disciplinary treatment discussion. After the tumor shrunk, resection of the rectal gastrointestinal stromal tumor was performed through the posterior vaginal wall. Adjuvant therapy was applied and no recurrence or metastasis has been found by the last follow-up on December 13, 2019. Transperineal CNB guided by ERUS and CEUS is a safe and effective preoperative biopsy of rectal SELs yet with some limitations.