Mulago National Referral Hospital is a public institution under Ministry of Health. There is an interim management board that offers an oversight function on behalf of the Ministry of Health.

There is a top management team, responsible for the day-to-day administration of the hospital headed by the executive director.

Management of the hospital is structured into seven directories: Obstetrics and Gynecology; Medical Services; Surgical Services; Diagnostics and Therapeutics; Private Patients Services; Pediatrics and Child health; Support Services