The University started education in the 1997-1998 academic year following the ratification of the "Agreement between the Republic of Turkey and the Government of the Kyrgyz Republic on the establishment of Kyrgyz-Turkish Manas University in Bishkek, the capital of Kyrgyzstan" signed in Izmir on September 30, 1995, by the competent authorities of both countries.

The university accepts students from Kyrgyzstan, Turkey, and other countries, especially the Turkic Republics and Related Communities.

Acceptance of students from Kyrgyzstan is based on the results of the Student Selection and Placement Examination (Manas-ÖSYS) and the Kyrgyzstan General State Examination (ORT) that the University conducts every year. Applicants from Turkey are also selected by the Student Selection and Placement Center of the Republic of Turkey (ÖSYM). Also, acceptance of students from Turkic Republics and Related Communities outside Kyrgyzstan and Turkey is possible under the coordination of the Commission on Student Admission from Turkic Republics and Related Communities established by the Rectorate.

In the 2022-2023 academic year, 5622 students, including preparatory classes, in 11 faculties, 1 high school, 1 vocational high school, and 430 students in master`s and doctoral programs received higher education.

The university is an autonomous university with the same status as state universities in Turkey and Kyrgyzstan.

Education at Manas University, which adopts student orientation as a principle within an academic discipline, is free of charge. Scholarships are also given to students if they meet the conditions. In addition, Credit and Dormitory Institutions in Turkey offer scholarships and loans to university students from the Republic of Turkey. The university provides high-quality food services for students. The Martyr Eren Bulbul Healthcare Center on the Chyngyz Aitmatov Campus provides comprehensive health services with a high priority on hygiene. Students can live in Student Dormitories, which have hot water and internet 24 hours a day. The language of instruction at the university is Turkish and Kyrgyz. In addition, some programs offer instruction in Russian, English, and Chinese.

Students graduate from faculties with a 4-year education period with a bachelor's degree and from vocational high schools with a 2-year education period with an associate's degree. The Faculty of Veterinary Medicine, which has a 5-year education period, gives its graduates the title of “veterinarian” and a “master's” diploma.