Kitovu Health Care Complex was founded in 1955, when the late Arch Bishop Joseph Kiwanuka, the first African Bishop South of the Sahara, invited the Religious Congregation of the Medical Missionaries of Mary Sisters (M.M.M.) from Ireland to build up a small First Aid Post in Masaka, Uganda.

The M.M.M. Sisters ran the hospital from 1955 to December 15, 2001, when they handed over the responsibilities of the management to the indigenous Congregation of the Bannabiikira (Daughters of Mary) Sisters Bwanda Masaka.