The foundations of Tarsus University were laid in 1992 with the establishment of Tarsus Vocational School and Tarsus Vocational School of Health Services, which were affiliated with Mersin University. In 2001, Tarsus Technical Education Faculty was established, followed by Tarsus School of Applied Technology and Business Administration in 2005, Tarsus Technology Faculty in 2009, and the Faculty of Aviation and Space Sciences in 2015. Tarsus University was officially founded on May 18, 2018, as per the law numbered 7141 published in the Official Gazette, and with this law, the academic units affiliated with Mersin University were transferred to Tarsus University. Additionally, two new faculties and one institute were established: the Faculty of Economics and Administrative Sciences, the Faculty of Humanities and Social Sciences, and the Graduate Education Institute.

The Faculty of Engineering was established by the Presidential Decree published in the Official Gazette on April 18, 2019, and the School of Applied Technology and Business Administration was closed and replaced by the Faculty of Applied Sciences by the Presidential Decree published in the Official Gazette on June 25, 2019. The Faculty of Health Sciences was established by the Presidential Decree published in the Official Gazette on January 8, 2020, and the Mersin Tarsus Organized Industrial Zone Technical Sciences Vocational School was established by the decision of the General Assembly of Higher Education on May 21, 2020. Finally, the School of Foreign Languages was established by the Presidential Decree published in the Official Gazette on June 29, 2021. Thus, Tarsus University comprises 1 institute, 7 faculties, 1 school, and 3 vocational schools.