Background The bowel is the most common site of extragenital endometriosis, with involvement of the locoregional sigmoid colon and anterior rectum seen most often. The clinical presentation varies depending on how soon patients seek medical care, thus requiring changes in management strategies. Endometriosis can cause a life-threatening surgical emergency with progressive obliteration of the bowel lumen leading to obstruction and late complications including toxic megacolon and transmural necrosis. Case presentation We report the case of a 41-year-old woman presenting with an acute abdomen and complete large bowel obstruction complicated by sepsis and toxic megacolon. The patient underwent emergency total colectomy with ileostomy. Medical history was significant for chronic, vague, and episodic lower abdominal pain self-medicated with herbal tea and laxatives. Pathologic examination demonstrated colonic endometriosis within the bowel wall as the cause of obstruction, ischemia, and transmural necrosis. Conclusions Although a rare clinical entity, this case highlights two important points. First, it demonstrates the value of performing proper and complete clinical work up to rule out or in all possible causes of colonic obstruction, including intestinal endometriosis. Second, it suggests a potential benefit of a formalized multidisciplinary approach, including surgery, in the management of medically unresponsive endometriosis. In conclusion, this case shows that endometriosis can cause life-threatening colonic obstruction in women of childbearing age. Prompt early intervention is warranted, particularly when obstruction is only partial and ischemia has not supervened, to conceivably prevent the development of a toxic megacolon requiring colectomy and avoid late complications.