The university offers graduate, masters, and doctoral programs.

The Ataturk-Alatoo University was affiliated and funded by Fethullah Gülen and his group advocating global Islamic education.

[1] Following the failed 2016 Turkish coup d'état attempt, which the Turkish government blamed on Gülen, the university changed its name from the International Atatürk-Alatoo University to the Ala-Too International University, appointed a Kyrgyz rector, and generally started to position itself more as a local institution.

The Ala-Too International University was established as the International Atatürk-Alatoo University in 1996 by the Sebat Educational Foundation which promotes and follows the tenets of Islam espoused by Fethullah Gülen.

[4] In February 2017, the Turkish government announced that diplomas issued by the Ala-Too International University would no longer be valid in Turkey.