The University of Muhammadiyah Makassar was founded on June 19th 1963 as the branch of the University of Muhammadiyah Jakarta. The establishment of this College was the realization of the results of the 21st Deliberation of Muhammadiyahꞌs Regional Council of South and Southeast Sulawesi in Bantaeng district.

The establishment was supported by the unity of Muhammadiyah as an organization engaged in education and teaching of missionary endeavor for amar maꞌruf nahi munkar, based on the letter number: E-6/098/1963 dated on 22nd Jumadil Akhir 1394 H/12th July 1963 M. Then, the founding certificate was made by the Notary Public, i.e., R. Sinojo Wongsowidjojo based on notaryꞌs deed No: 71 dated on June 19th, 1963. The University of Muhammadiyah Makassar was declared as the Private University registered since October 1st, 1965.

The University of Muhammadiyah Makassar (Unismuh Makassar) as the one of Muhammadiyah Universities (PTM) assigns the task and a very important role for religious, the nation and state, both in the present and in the future. Besides its position as one of the Muhammadiyah Universities or the Private Universities (PTM/PTS) in Eastern Indonesia which is relatively as a great university, it is also embedded the educational culture which is inherited as charitable efforts of Muhammadiyah. The name of Muhammadiyah, which is integrated with the name of Makassar, gives the hope for integrated culture, scientific, and religious breath.

At its inception, the University of Muhammadiyah Makassar built two faculties, namely the Faculty of Teacher Training and Arts Department of Indonesia, and the Faculty of Teacher Training and Educational Sciences Department of Public Education (PU), and Social Studies (PS) which were led by the Rector, i.e., Dr. H. Sudan. In the same year (1963), the University of Muhammadiyah Makassar has stood on its own and is chaired by the Rector of Drs. H. Abdul Watif Masri.

The next development of the University of Muhammadiyah Makassar in 1995, it opened the new faculties, namely: the Faculty of Religious Studies and Dakwah (FIAD), the Faculty of Economics (Fekon), the Faculty of Social Welfare, and Academy of Agriculture. Furthermore, it opened the Faculty of Engineering in 1987, the Faculty of Agriculture in 1994, the Graduate Program in 2002, and the Faculty of Medicine in 2008, and until now, the University of Muhammadiyah Makassar has had 7 faculties, 34 study programs and Graduate Program which have been accredited by BAN-PT.

In 2003, the University of Muhammadiyah Makassar encountered the transitional stage of historical development, such as in the form changing of leadership formation by merger of the younger generation and the older generation. The leadership and the entire academic staff of Muhammadiyah Makassar University were determined to preserve the achievements of its predecessors and develop it to the better outcomes, as well as committed: (1) maintaining public confidence, (2) achieving the excellence in the increasingly fierce competition, and (3) realizing independence in the management and self-development. The third commitments are expected to present the University of Muhammadiyah Makassar became the foremost Islamic College.