The Hospital is currently governed by a Board of Governors (BOG) appointed by the Chairperson of the Registered Trustees of Kabale Diocese, the Bishop of the Diocese, currently, the Right Reverend Bishop Callist Rubaramira. The Hospital is run on a day-to-day basis by a management team appointed as outlined in the Hospital Charter. The Hospital is comprised of five (5) primary departments: Medical, Nursing, Administration, Training and Community Health. The latter has for long served as the headquarters of Bufumbira East health sub-district until this mandate was withdrawn by the district under circumstances that are poorly understood. The medical section in turn consists of the medical wards (male and female), male surgical ward, female surgical ward, paediatric ward, maternity ward, gynaecological ward with their support departments: X-ray, laboratory and Pharmacy.

Mutolere hospital is a general hospital providing both outpatient and inpatient services. The outpatient department runs specialized clinics in ophthalmology and HIV/AIDS. The inpatient services are organized into four major wards: medical, surgical, pediatrics and maternity. It has full time specialist in Obstetrics and gynecology and visiting surgeons from Holland.

As a health services provider as well as a contributor to the national pool of human resources for health, the hospital and its training wing have continued to achieve and contribute to the country’s national health-care system.