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.
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.