In 1961, the Ministry of Religious Affairs founded branches of IAIN Sunan Kalijaga Yogyakarta in the cities of Surabaya and Malang.

Later on, the three were merged into IAIN Sunan Ampel before the Malang branch separated in 1997, due to a presidential decree mandating the creation of separate Islamic institutes (referred to as Sekolah Tinggi Agama Islam Negeri or STAIN) across the country.

[6] In 2009, Susilo Bambang Yudhoyono once more altered the university's name - this time to Universitas Islam Negeri Maulana Malik Ibrahim Malang, based from Wali Songo member Malik Ibrahim.

This further name change was preceded by a massive expansion of university facilities, partly funded by the Islamic Development Bank.

[5] Compared to Brawijaya University and Malang State University, UIN Maliki takes in the fewest freshmen annually, with 2,500 students in 2014 compared to over 12,000 for Brawijaya and about 7,000 for Malang State.