State Islamic University (UIN) Sunan Kalijaga Yogyakarta was born as a continuation of the State Islamic College (PTAIN), the Academy of Religious Sciences (ADIA), and the State Islamic Institute (IAIN). Its birth aims to explore Islamic teachings and develop the nation's spiritual treasures as a process of the struggle of the Indonesian people and to participate in filling and realizing the ideals of Indonesian Independence, namely to advance public welfare and educate the nation's life.

UIN Sunan Kalijaga as an Islamic Higher Education institution (PTAI) realizes that the universality of Islam must accept the reality of the nation's pluralism and the process of globalization in the midst of international relations. This reality requires UIN Sunan Kalijaga to be morally and academically responsible for studying Islam; spreading peace and communicating it to the entire world community through the Tri Dharma of Higher Education; and empowering human resources who are experts in Islamic Religious Studies, faithful, and pious.
Since the 1983/1984 Academic Year, UIN Sunan Kalijaga has pioneered formal education for scholars who wish to obtain Masters and Doctoral degrees. This pioneering is based on the Decree of the Minister of Religion No. 26 of 1983 which was re-established by Decree of the Minister of Religious Affairs No. 208 of 1997 and Decree of the Minister of Religious Affairs No. 95 of 1999. In the 1985/1986 Academic Year, for the first time, the Postgraduate Program produced Masters graduates and from that time on, Doctoral Program (S3) lecture activities were also carried out.

This formal education was initially called the Faculty of Postgraduate and Doctoral Education of IAIN Sunan Kalijaga Yogyakarta. Furthermore, for the first time, the dean of the Faculty of Postgraduate and Doctoral Education was held by the Rector of IAIN Sunan Kalijaga Yogyakarta, H. Zaini Dahlan, M.A.
Not long after serving as dean, H. Zaini Dahlan, M.A. was appointed by the Indonesian government as Director General of Islamic Religious Institutional Development of the Ministry of Religious Affairs. Furthermore, the position of dean of the Faculty of Postgraduate and Doctoral Education was delegated to Prof. Dr. Hj. Zakiah Daradjat.

In further developments, the name of the Faculty of Postgraduate and Doctoral Education was changed to the Postgraduate Program led by a director. For the first time, the position of Director of the Postgraduate Program at IAIN Sunan Kalijaga was held by Prof. Dr. H. Nourouzzaman Shiddiqi, M.A. However, on July 16, 1999, he passed away. Furthermore, the Acting Director of the Postgraduate Program at IAIN Sunan Kalijaga was concurrently held by the Rector of IAIN Sunan Kalijaga Yogyakarta, Prof. Dr. H. M. Atho Mudzhar, based on the Decree of the Rector of IAIN Sunan Kalijaga, Number: 198/Ba.0/A/1999.

Furthermore, in the following year on February 7, 2000, Prof. Dr. Faisal Ismail, M.A. was appointed as the new Director of the Postgraduate Program at IAIN Sunan Kalijaga, based on the Decree of the Rector of IAIN Sunan Kalijaga, Number: 21/Ba.0/A/2000. After four months as Director, he was appointed by the President of the Republic of Indonesia as Head of the Religious Research and Development Agency of the Department of Religious Affairs in Jakarta.

In accordance with the Explanation of Article 54 paragraph (1) of Government Regulation No. 60 of 1999, starting from June 12, 2000, with the Decree of the Rector, the Acting Director of the Postgraduate Program of IAIN Sunan Kalijaga was concurrently held by the Vice Rector I, Prof. Dr. H. M. Amin Abdullah, based on the Decree of the Rector of IAIN Sunan Kalijaga, Number: 91/Ba.0/A/2000.

With the election of Prof. Dr. H. M. Amin Abdullah as the Rector of IAIN Sunan Kalijaga, based on the Decree of the Rector Number 115/Ba.0/A/2002, effective from March 22, 2002, the Director of the Postgraduate Program of IAIN Sunan Kalijaga was held by Prof. Dr. H. Musa Asy’arie.

Before his term of office ended, Prof. Dr. H. Musa Asy’arie was appointed as Expert Staff of the Minister of Communication and Information for Social Culture and Community Role, based on the Decree of the President of the Republic of Indonesia Number 81/M of 2005 dated May 23, 2005. Furthermore, between 2005 and 2006, the Acting Director of the Postgraduate Program at UIN Sunan Kalijaga was held by Prof. Dr. H. Machasin, M.A., based on the Decree of the Rector of UIN Sunan Kalijaga, Number: 218/Ba.0/A/2005.

Furthermore, starting from July 17, 2006 to 2010, the Director of the Postgraduate Program at UIN Sunan Kalijaga was held by Prof. Dr. H. Iskandar Zulkarnain. This was based on the Decree of the Rector of UIN Sunan Kalijaga Yogyakarta, Number: 312/Ba.0/A/2006.

Starting in 2001/2002, the UIN Sunan Kalijaga Postgraduate Program implemented the Integrated Curriculum for Masters/Doctoral Degrees. The system used is full, each student is free to choose the courses offered by fulfilling the number of credits that have been set. Along with the transformation of UIN based on Presidential Decree No. 50 dated June 21, 2004, this institution also changed to the UIN Sunan Kalijaga Postgraduate Program.