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.

　　本學系原名生物學系，於民國79年10月9日獲教育部核定准予籌備，於民國80年8月1日成立，為全國第一所設立於醫學系統院校的生物學系。首屆招收一般新生50名，83學年度起增收推薦甄選新生，民國84年第一屆學生畢業。民國88年本校改制為醫學大學，本學系隸屬於生命科學院，92學年度經教育部核准更名為生物醫學暨環境生物學系。民國94年成立碩士班，首度招收碩士班學生5名，民國98年設置學士班學生預修碩士班課程制度，目前每年招收研究生名額已增加到10名，並另有招收外籍生名額1名。

　　本學系申請教育部『強化與東協及南亞國家合作交流以個別學校辦理之計畫」於民國110年9月9日核准成立「資料科學於生物與生醫應用新南向B區博士專班」，預計於111學年度開始招生。