The Fisheries Centre was founded in 1992 as a research unit within the Faculty of Graduate Studies to facilitate and foster research and training in freshwater and marine fisheries' scientific, social, and legal aspects. However, its origins date back to 1953 with the establishment of the Institute of Fisheries. According to the 1953/54 UBC Calendar, the Institute's objective was "to give, at the graduate level, broad and advanced instruction in various fields relating to the best use and management of the fisheries resources... [including] biology, economics, law, commerce, engineering, nutrition, technology, etc." By 1959 its programmes had expanded to include cooperation with the Vancouver Public Aquarium, the federal Pacific Fisheries Experimental Station, and the UBC Institute of Oceanography. The Institute's name changed to Animal Resource Ecology in 1970. It made this change reflect its expanded focus on "theoretical ecology, applied ecology and population genetics and relate them to specific ecological systems - freshwater and marine communities, mammal, bird, fish and insect populations and human systems" (1970/71 UBC Calendar). The Institute's activities remained closely tied to those of the Department of Zoology. It also interacted with Agricultural Sciences, Forestry, and Community and Regional Planning. The Institute was discontinued in 1988 but re-established as the Fisheries Centre in 1992. In 2000 the Centre was re-organized into two sections: the B.C. Fisheries Research Section, and the Marine Mammal Research Unit.
The directors of the Institute of Fisheries / Animal Resource Ecology were: W.A. Clemens (1953-55), Peter A. Larkin (1955-63, 1966-69), Norman J. Wilimovsky (1964-66), C.S. Holling (1970-75), W.G. Wellington (1975-80), J.D. McPhail (1980-81, 1986-88), and C.C. Lindsey (1981-86). Since its re-establishment, the Fisheries Centre's directors have been L.M. Lavkulich (acting, 1992-93) and T.J. Pitcher (1993- ).