An inverted (intussuscepted) appendix is a rare finding, often mistaken for a polyp as it presents with vague symptoms. This can result in misdiagnosis and inappropriate management. Diagnosis is usually made through surgery. Rarely, endometriosis has been found as the cause of the intussusception. A 42-year-old woman presented with frequent loose stools over 2 years, an elevated calprotectin over 400 μg/g faeces (normal <110) and a serum C-reactive protein of 40 mg/l (normal <5 mg/l). Endoscopy showed an inverted appendix. Histopathology results showed inflammation and ulceration. Laparoscopic appendicectomy was performed successfully, and endometriosis was found on the inverted appendix. This is the first case reported of an inverted appendix containing endometriosis, in which the intussusception of the appendix has been diagnosed on endoscopy. This case highlights how endometriosis can involve just the appendix, without any involvement of reproductive organs. We suggest considering inverted appendix as a differential diagnosis when investigating caecal lesions.