We report a case of a 48-year-old male with HIV and poor adherence to antiretroviral therapy, presenting with two months of abdominal pain and diarrhea. His latest CD4 count was 11/µL. Imaging and biopsy confirmed CMV enteritis with ulcerated lesions in the distal ileum. Despite prolonged antiviral therapy with ganciclovir and foscarnet, the patient's condition remained refractory, necessitating ileocaecal resection and ileostomy, followed by further resection and anastomosis. Post-surgery, the patient recovered well and was discharged. This case underscores the potential benefit of surgical intervention in CMV enteritis unresponsive to medical treatment in HIV patients.