The Department was founded in 1990 as the Department of Environmental Engineering and Health, Chia Nan Junior College of Pharmacy. In 1996, the College was upgraded by the Ministry of Education to become Chia Nan College of Pharmacy and Science, and in 2000 was formally accredited with full university status, becoming Chia Nan University of Pharmacy and Science. The Master Degree Program was established in 2001. In 2003, the Department was renamed as the Department of Environmental Engineering and Science.