National Chiayi University was formed in February 2000 by merging two existing colleges in Chiayi, i.e., National Chiayi Institute of Technology (NCIT) and National Chiayi Teachers College(NCTC). The University now has seven colleges (Teachers College, College of Humanities and Arts, College of Management, College of Agriculture, College of Science and Engineering, College of Life Sciences and College of Veterinary Medicine), which include 39 undergraduate programs (40 departments), 12 in-service undergraduate programs(1 program, 39 master programs(42 classes), 14 in-service master programs, and 7 doctoral programs(1 program)  in the 107 semester year. NCYU is one of the oldest and largest universities in the southern part of Taiwan.

National Chiayi Institute of Technology was first founded in April, 1919 as ″Chiayi Agriculture and Forestry Public School″. It was reorganized and named as “Taiwan Provincial Chiayi Agri-Vocational School” in November, 1945. In March, 1965, the School was upgraded and became “Taiwan Provincial Chiayi Junior College of Agriculture.” In July, 1981, and the college became a national college directly funded by the Ministry of Education. In July, 1997, the college was upgraded again to a college and became “National Chiayi Institute of Technology.” In its 90 year history, the College has trained professionals in different fields.

National Chiayi Teachers College was first founded in 1957 as ″Taiwan Provincial Chiayi Normal School″. The school recruited junior high school graduates and trained them as kindergarten and elementary school teachers. In August, 1996, the School was upgraded to a five-year junior college and renamed as ″Taiwan Provincial Chiayi Junior Teachers College.” The College was reformed , into a four-year college, and renamed as ″Taiwan Provincial Chiayi Teachers College″ in July, 1987. In July, 1991, the College became a national college and was renamed as ″National Chiayi Teachers College.″ Since it was established in 1957, the College has trained thousands of elementary and kindergarten teachers, most of them have taught in schools all over the country or served in education related public sectors.

By merging the two colleges, National Chiayi University is one of the few comprehensive universities in the southwestern part of Taiwan, covering a wide range of domains, including Life Science, Agriculture, Management, Science and Engineering, Humanities and Arts, and Education.