June 10, 1989 marks the history of PUP, it is the date when Hon. Leopoldo M. Laurel, Jr., Municipal Mayor of Santo Tomas envisioned the dreams of establishing a branch in the town by sending a letter of interest and appreciation to Dr. Nemesio E. Prudente, President of PUP. Dr. Dante G. Guevarra initiated the proposal. A deed of donation for a one hectare municipal land was done through Resolution No. 89-18 following the groundbreaking rites on 28 January 1991.

The first office of the director of PUP Santo Tomas was located at the Santo Tomas municipal building and later transferred to the one-story building that also housed the first batch of students, the Lions Club Building.

In school year 1992-1993, the branch accepted the first batch of students with a total number of 292. The courses offered during the year were: Bachelor of Business Administration, Bachelor of Accountancy, Bachelor of Computer Data Processing Management, Bachelor of Office Administration and Bachelor of Electronic and Communication Engineering.

In March 2001, an act passed by the Congress, the R.A. No. 9045, or the act which creates the Batangas State University by integrating different public higher education institutions in Batangas province including PUP Santo Tomas. This led to the protest of the PUP Santo Tomas community not to be part of the Batangas State University, for students of the PUP Santo Tomas will lose the privilege to study at the cheapest cost. The university officials together with faculty, staff and students blocked the entry of the BSU officials into the campus. They also petitioned to the congress to amend R.A. 9045 excluding to its coverage the PUP Santo Tomas.

In May 2007, Republic Act 9472 was ratified, excluding the PUP Santo Tomas Campus from the coverage of the Batangas State University.