The Institute was founded in September 1959 when it was incorporated as a non-profit company and affiliated with the University of Cape Town. Both in conception and realisation, the Fitztitute was largely the product of the vision of one person, Mrs Cecily Niven, daughter of the late and famous Sir Percy FitzPatrick. The Fitztitute was founded with two objectives in mind: firstly the understanding of the living bird; secondly, the housing in perpetuity of the ornithological records and literature essential to sound research. These objectives remain central to the philosophy of the Institute.
In 1960, JM Winterbottom assumed office as first director of the Institute. Roy Siegfried became the Fitztitute's second director in 1973 when Prof Winterbottom retired, and under his directorship built up the Fitztitute's international reputation for the research and teaching of both ornithology and conservation biology. Shortly after, the Fitztitute and SAFRING (the South African Bird Ringing Unit) became formally incorporated within the University of Cape Town as an autonomous subunit within the department of Zoology. SAFRING moved into the department of Statistical Sciences in 1989, taking with it the now complete Southern African Bird Atlas Project. Morné du Plessis took up the Directorship of the Institute in 1996 after Roy Siegfried's retirement at the end of 1995. Phil Hockey was appointed as the Institute's new Director in July 2008 having taken on the role of Acting Director following Morné du Plessis' departure for WWF in August 2007. Peter Ryan became Director after Phil's death in January 2013.
Since its inception in 1960, the Percy FitzPatrick Institute of African Ornithology has developed into the largest centre for ornithological research in the Southern Hemisphere. During its first decade, much research effort was devoted to faunistic surveys and general studies of individual species. This work culminated in comprehensive descriptive reviews of the ecological distribution and zoogeography of the southern African avifauna, as well as in the monographs of the life histories of numerous species. Increasingly in recent years the Fitztitute has been called on to undertake research dealing with environmental problems and the exploitation of biological resources, and to advise government and private sector bodies accordingly.