The Department was formerly known as the department of biology and was approved by the Ministry of Education on October 9, 1990 for preparation. The department was established on August 1, 1991 and was the first department of biology set up in a medical school in Taiwan. The department admitted 50 regular freshmen in the first year. Starting from 1994, the department admitted freshmen through recommendation and screening. The first class of the department graduated in 1995 and the school then was restricted to a medical university in 1999. The department belonged to the college of life science and was then approved by the Ministry of Education in 1993 to rename was the Department of Biomedical Science and Environmental Biology. In 2005, the department offered the master's program and admitted 5 students to the master's program for the first time. In 2007, the department offered the preparatory course system of the master's program for undergraduate students and currently the number of graduate students admitted each year is 10 now with additional admission for one international student.

The department has applied for the “Proposal for strengthening cooperation and exchange program by individual school- ASEAN and South Asian countries” and was approved by the Ministry of Education on September 9, 2021, to establish the “Informatics in Biology and Biomedical Applications for New Southbound Zone B Doctoral Program.” The program is expected accept admission applications for the 2022 academic year.