Cebu Technological University Carmen was the then Quirino School of Fisheries (QSF) created under Republic Act 2700 in 1959, whose mandate was to offer a four-year secondary fisheries curriculum. However, it was only in 1961 that it formally started operating as a secondary fishery school under the Department of Education Culture and Sports (DECS), admitting 67 students with Three (3) teachers and a principal. In 1964 the Administration and Supervision of the school were transferred from DECS to Cebu School of Arts and Trades (CSAT). By the Bureau of Vocational Education (BVE) Circular No. 2 series of 1974, the school was authorized to offer a three-year post-secondary fishery technical education curriculum leading to the Diploma in Fishery Technology, returning its administration and supervision to DECS.
In 1978, under the Ministry of Education Culture and Sports (MECS) Order No. 72, the school was converted into a Regional Institute of Fisheries Technology (RIFT), one of the seven such schools recommended by the Educational Development Projects Implementing Task Force (EDPITAF) under the 6th Education Loan (1978 PH World Bank Loan). In 1982, the PhP 38-Million Building Complex, a component of the foreign-assisted fishery education project undertaken through EDPITAF, was started. Items in the Building Complex include Academic and Administration, Dormitory, Marine Fisheries Laboratory, Fish Processing, Mess Hall, Fish Mill, Fish Capture, Staff Houses and Apartments, Water Tank, Power, and Guard Houses.
In June 1983 was the enrollment of the first batch of students under the foreign assisted fishery education. In the same year under Batas Pambansa Bilang 412, the school became the College of Fisheries Technology- Carmen Campus of the Cebu State College of Science and Technology (CSCST). At the same time, it continued to operate as a Regional Institute of Fisheries Technology, implementing the World bank assisted Fishery-Education Curriculum leading to the Diploma in Fisheries Technology (DFT). In 1995, the school continued to offer the BS Marine Engineering Program offered by CSCST-Main Campus. Thus, it admitted the first batch of 40 male students. The Bachelor of Science in Fisheries majors in Fish Processing, Capture Fisheries, and Aquaculture Technology commenced in 1996 following the approved curriculum program of CSCST-Moalboal Campus. Additional Baccalaureate degree programs were opened in the year 2000 for the BS Education, 2003 for BSHRST, and the offering of the other degree programs followed.
By enacting Republic Act 9744, the Cebu State College of Science and Technology was converted into Cebu Technological University in 2009, expanding its curricular offering from Baccalaureate to graduate programs in Education, Fisheries, and Aquatic Sciences. As a result, the different curricular offerings of Carmen Campus gained Levels II and III (phase1) accreditation from the Accrediting Agency of Chartered Colleges and Universities in the Philippines (AACCUP) apart from being an ISO 9001:2015 Certificated.
Under the stewardship of Dr. Rosein A. Ancheta Jr., the university is now a Quacquarelli Symonds (QS) Three (3) Stars University.