Endometriosis is a relatively common gynecological condition in women of reproductive age. The rectosigmoid region is the most commonly affected segment when the gastrointestinal tract is involved. A differential diagnosis of colorectal neoplasia is difficult because of the similar clinical, endoscopic, and radiology findings. A 42-year-old female presented with abdominal distention and was subsequently diagnosed with a large bowel obstruction in the rectum. A temporary colostomy was performed, and endoscopy revealed a rectal mass obstructing the rectum. The biopsy showed normal mucosa, and it was difficult to exclude rectal malignancies even after the imaging workup. Endoscopic ultrasound demonstrated a hypoechoic lesion below the rectal mucosa, and fine needle aspiration confirmed the diagnosis of bowel endometriosis. Bowel endometriosis is a challenging diagnosis. Endoscopic ultrasound-guided fine-needle aspiration is useful for acquiring adequate samples for histological confirmation and a definitive diagnosis of bowel endometriosis.