BISU Clarin has its roots as the Clarin School of Fisheries. Formerly Clarin Junior High School, It was founded in 1949. From the general secondary curriculum, it was converted to a vocational secondary (Fishery) school under the Bureau of Vocational Education in July 1, 1962 by virtue of Republic Act 2834 through the bill passed at the congress by former Congressman Bartolome Cabangbang. This fourth national vocational school in the province of Bohol started its operation in one semi-concrete building situated in an area of 61, 656 sq. meters. Fifteen (15) personnel ran the office with the appropriation of P50,000.00.

In the year 1967, the late President Ferdinand E. Marcos signed the National Reservation 193 under Proclamation no. 209-A declaring the area of 9.2361 hectares along the shore of Clarin as an additional site of Clarin School of Fisheries (CSF). The School then has acquired twelve buildings with 25 classrooms, a library, conference hall, school clinic, a guidance center and offices  of the administrative staff. A standard basketball court, twin tennis courts, and a spacious cafeteria were functional, catering to students, teachers and outsiders as well. In 1994, another two-room shop building was completed.

During the school year 1975-1976, the Clarin School of Fisheries got the approval of the Ministry of Education, Culture and Sports to offer technical courses leading to the Diploma in Fishery Technology (DFT). Then in 1992 the school offered Agricultural Technician Course (ATC).

On June 22, 1998, by Virtue of Republic Act 8659, Central Visayas State College of Agriculture, Forestry and Technology (CVSCAFT) was established. Clarin School of Fisheries was integrated to other four vocational schools in Bohol; Bohol School of Arts and Trades in Tagbilaran City, Bohol School of Fisheries in Candijay, and Calape National School of Fisheries in Calape. CVSCAFT was managed under the leadership of Dr. Mateo M. Limbago, the 1st College President.

CVSCAFT Clarin Campus occupied a wide inland and fishpond areas. It is approximately 300 meters from the municipal landmark of Clarin, Bohol and it is 61 kilometers away from Tagbilaran City. It occupies a total land area of 27.3439 hectares inclusive of the 12 hectares fishpond.

On October 14, 2009, CVSCAFT, its units and satellite campuses, was converted into a State University  known as Bohol Island State University (BISU) under the Republic Act No. 9722 duly signed and approved by former President, Her Excellency Gloria Macapagal-Arroyo. The Bill was authored by Congressmen: Hon. Edgar M. Chatto, Hon. Roberto C. Cajes, Hon. Adam Relson L. Jala, et al. Its first University President is Dr. Elpidio T. Magante, Ed. D., C.E., who holds office at the Main Campus, Tagbilaran City.