The Pontifical and Royal Catholic University of Santo Tomas, the Catholic University of the Philippines, holds the distinction of being the first to introduce the degree of Bachelor of Science in Biochemistry under the Faculty of Pharmacy. On April 17, 1962, Rev. Fr. Lorenzo Rodriguez, O.P., the Dean of the Faculty of Pharmacy from 1946 to 1968, chaired the Committee initiating the proposal of a 5-year curriculum leading to the degree of Bachelor of Science in Biochemistry. In 1967, 42 students graduated from the program.

In 1985, a 4-year curriculum was introduced to address the changing needs of the time. The program aims to equip the students with the understanding of the chemical and molecular principles in the study of biological systems and their applications in the allied health, biological and environmental sciences.

In 2015, the Department of Biochemistry was granted a Level 1 Program Accreditation Status by the PACUCOA and the FAAP. The department was assessed for Level 2 Program Accreditation by the PACUCOA last September 2017. In 2018, the BS Biochemistry program received its first international certification, from the ASEAN University Network Quality Assurance Group.