Starting in 1964 as Mindanao State University Preparatory High School in Bongao, Tawi-Tawi, a mere adjunct to MSU Marawi Preparatory High School, MSU Tawi-Tawi College of Technology and Oceanography has grown into an institution of academic excellence. More secondary schools were established from 1967 to 1977 in the outlying island municipalities of Tawi-Tawi. By 1990, 20 high schools were put up throughout the province. In 1984, MSU-TCTO Science High School and MSU-TCTO Child Development Center – Laboratory Elementary School were established.

Republic Act 6060 gave birth to MSU-Sulu College of Technology and Oceanography on August 4, 1969, initially offering degree programs and diploma in Fisheries Technology.

In  1973,  Tawi-Tawi  became  a  separate  province  from  Sulu,  and  MSU-SCTO

became MSU-Tawi-Tawi College of Technology and Oceanography per BP Blg. 197. In

1990 it became an autonomous university campus.

In its more than four decades of existence, it has steadfastly pursued its vision to be the center of excellence in Fisheries, Marine and Maritime Sciences and Engineering, and Oceanography, in its mission to give Muslims and other cultural minorities access to quality education and develop such other programs as will promote Muslim welfare and hasten socio-economic development of the southernmost region of the country.

MSU-TCTO is comprised of the following academic units: the Graduate School, College of Fisheries, College of Arts and Sciences, College of Education,  Institute of Environmental and Oceanography Studies, College of Islamic and Arabic Studies, and the Institute of Information and Communications Technology.

The  extension  services  of  the  college  include  providing  capability  building trainings and functional literacy programs to the Tawi-Tawians. The local folks are empowered through education and entrepreneurial development.

The college has continued to undertake researches in fisheries aquaculture, and marine related sciences, as well as in the social sciences. These initiatives are designed to promote sustainable utilization and rational management of the marine and fisheries resources of the area, with the aim of improving the standard of living of the people of Southern Philippines.