The Academy of Islamic Studies University of Malaya as it exists today is the result of a merger between the Department of Islamic Studies and the Academy of Islam. Prior to this merging both were independent institutions within the University of Malaya . The Department of Islamic Studies was formed in 1959 as a result of a formal relationship between the then Islamic College of Malaya and the University of Malaya. Since then the Council for Islamic Colleges functioned as the executive controller to the Department whilst the Senate of the University of Malaya monitors all academic matters. When the Council of Islamic Colleges was dissolved in 1970 the Department of Islamic Studies was placed under the purview of the Council and Senate of the University of Malaya. From that point until the time of its merger with the Academy of Islamic Studies in April 1996 this Department was a department under the Faculty of Arts and Social Sciences University of Malaya.

As for the Academy of Islam it was formed in 1981 as a result of the taking over of the Kelantan Foundation for Higher Islamic Studies which was established in 1965. The Academy consisted of two faculties–namely the Faculty of Syariah and the Faculty of Usuluddin — one degree programme — the Bachelors in Islamic Education Degree — and one matriculation programme the Pre-Academy of Islam. In 1996 the Academy continued to grow with the formation of 9 Departments which were divided across four divisions which are the Division of Syariah Studies that is made up of the Department of Fiqh and Usul the Department of Siasah Syar iyyah the Department of Syariah and Economics the Department of Syariah and Management and the Department of Syariah and Law. The Division of Theological Studies on the other hand comprised of the Department of Aqidah and Islamic Thoughts the Department of Missionary and Human Development the Department of Al-Quran and Al-Hadith and the Department of Islamic History and Civilization. The Division of Joined Studies conducted the Islamic Education and Islamic Studies programmes in other words continuing the joined studies programme with the Faculty of Arts and Social Sciences. The Pre-Academy Programme meanwhile also continued to be carried out at the Nilam Puri branch campus in Kelantan.