UP Visayas has two campuses—Miagao and Iloilo City — with Miagao being the main campus where the central administration offices are located.

During the term of UP President Onofre D. Corpuz in 1975 an interdisciplinary team within the university conceived of an autonomous unit which would become an institution for fisheries and marine science education and research.

The idea was fleshed out in a proposal entitled "Education Development Plan for the University of the Philippines in the Visayas", a six-volume report by the interdisciplinary team.

Funding was to come partly from a government loan, to be negotiated with the World Bank for the development of fisheries education.

On September 21, 1977, President Ferdinand E. Marcos issued Presidential Decree 1200, known as the Philippine Five-Year Development Plan (1978–1982), which provides, among others, that Region VI would be the site of the University of the Philippines in the Visayas (UPV) with emphasis on fisheries and marine sciences.

The fisheries educational loan was then re-negotiated with the World Bank inasmuch as its appraisal team had earlier favorably endorsed the development plan.

Through the Sixth Educational Loan of the Philippine Government approved by the World Bank in January 1980, the development of the UPV flagship college was made possible.

The development of the site and construction of facilities began in September 1981 and was made possible through the Sixth Educational Loan.

The loan of about $18 million was used for site acquisition, construction of buildings, procurement of equipment, and the transfer of the College of Fisheries personnel and other property from Diliman to Miagao.

In May 1988, the College of Fisheries transferred to the new site in Miagao under the leadership of Chancellor Rogelio O. Juliano and Dean Efren Ed.

The High School is an experimental laboratory for innovative teaching strategies designed to provide academic training for underprivileged students in order to better prepare them for access to tertiary education in the University of the Philippines.

At present, a Land Bank of the Philippines (LBP) Branch is accommodated in the UPV Miagao Campus Library-Museum Building.

The college has instituted degree programs that address the need for sustainable development of the country's fisheries resources and respond to the call for highly trained manpower in the field, at graduate and undergraduate level.

The college has a Division of Professional Education and a laboratory high school designed to train underprivileged youth especially from rural areas.

It was formally operationalized on February 17, 1986, with the transfer of the Food Technology program, along with its faculty, from the College of Arts and Sciences.

The objectives of the college are to support the UPV programs in fisheries, marine sciences, the arts, social and natural sciences; to provide management education in order to train leaders for the region's public and private sectors; to serve as center for research, information dissemination, consultancy, and training services in administration/management; and to serve as a link between UPV and local, national, and international organizations engaged in management education, training and research.

In July 1997, CM started the pilot testing of a course on Island Food Systems in RDM 298 (Field Studies), a course in the Master of Management, Rural Development Program.

The initiative was made under the auspices of the Island Sustainability, Livelihood, and Equity (ISLE) Program.