* National University of Tainan (國立臺南大學) NUTN used to be the Institute of Teachers' In-service Education in 1988, promoted and renamed National Tainan Teachers College in 1991. In 2004, it was established as National University of Tainan until now. The motto of NUTN includes benevolence, intelligence, sincerity and uprightness.
* National Cheng Kung University (國立成功大學), one of the leading universities in Taiwan, is located in the East District. It is famous for its engineering programs. In 1931, NCKU was established as Tainan Technical College, located on the present Cheng-Kung Campus, with a total area of 183,000 square metres. As the number of colleges expanded, it was upgraded to a provincial university in 1956, then national university in 1971. Today, National Cheng Kung University serves nearly 21,000 students through 9 colleges, 39 departments, and 49 graduate institutes.
* Tainan National University of the Arts (國立臺南藝術大學) TNNUA exists to prepare talented individuals for careers in visual and performing arts, sound and image design, building arts, conservation arts, and art history and critique. The university emphasizes learning through individual attention and independent work creation. It is a public institution first established in 1996.
* Tainan Theological College and Seminary (臺南神學院) was established in 1876 by Thomas Barclay.
* Chang Jung Christian University is a private university affiliated with the Presbyterian Church in Taiwan. CJU offers masters and doctoral degree programs and aims to promote fraternity, justice, and service for Taiwan. It is located south of the city, in Gueiren.
* Southern Taiwan University of Technology (南台科技大學), founded in 1969, is located near the northeastern border of Tainan City, within a 30-minute driving distance from the Tainan Airport.
* The Tainan University of Technology (臺南應用科技大學) is a private university founded in 1964. The university offers graduate degrees in music, visual art, and applied sciences.