The 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). His birth aims to explore the teachings of Islam and develop the spiritual treasures of the nation 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 the general welfare and educate the nation's life.

UIN Sunan Kalijaga as an Islamic Higher Education Institution (PTAI) realizes the universality of Islam and must accept the reality of national pluralism and the process of globalization in the midst of international relations. This fact 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 Religion, have faith, and are pious.

Since the Academic Year 1983/1984, UIN Sunan Kalijaga has initiated formal education for scholars who wish to obtain Masters and Doctoral degrees. This pilot is based on the Decree of the Minister of Religion No. 26 of 1983 which was redefined by the Decree of the Minister of Religion No. 208 of 1997 and the Decree of the Minister of Religion No. 95 of 1999. In the Academic Year of 1985/1986 for the first time the Postgraduate School gave birth to Master's graduates and from that moment on, Doctoral Program (S3) lectures were carried out.

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

In subsequent developments, the name of the Faculty of Postgraduate and Doctoral Education was changed to the Postgraduate School led by a director. For the first time, the position of Director of the Postgraduate School at IAIN Sunan Kalijaga is held by Prof. Dr. H. Nourouzzaman Shiddiqi, MA But on July 16, 1999, he died. Furthermore, the Acting Director of the Postgraduate School of IAIN Sunan Kalijaga concurrently with the Chancellor of IAIN Sunan Kalijaga Yogyakarta, Prof. Dr. HM Atho Mudzhar, based on the Decree of the Chancellor of IAIN Sunan Kalijaga, Number: 198/Ba.0/A/1999.

Furthermore, in the following year on February 7, 2000, Prof. Dr. Faisal Ismail, MA was appointed as the new Director of the Postgraduate School at IAIN Sunan Kalijaga, based on the Decree of the Chancellor 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 Ministry of Religion in Jakarta.

In accordance with the Elucidation of Article 54 paragraph (1) Government Regulation no. 60 of 1999, starting on June 12, 2000, by Decree of the Chancellor, Acting. The Director of the Postgraduate School at IAIN Sunan Kalijaga concurrently with the Vice-Chancellor I, Prof. Dr. HM Amin Abdullah, based on the Decree of the Chancellor of IAIN Sunan Kalijaga, Number: 91/Ba.0/A/2000.

With the election of Prof. Dr. HM Amin Abdullah as Chancellor of IAIN Sunan Kalijaga, based on the Rector's decision Number 115/Ba.0/A/2002, as of March 22, 2002, the Postgraduate School Director of IAIN Sunan Kalijaga is 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 to the Minister of Communication and Informatics, Socio-Cultural and Community Roles, based on the Decree of the President of the Republic of Indonesia Number 81/M of 2005 dated May 23, 2005. Furthermore, the period between 2005 and 2006, Acting Director of the Postgraduate School of UIN Sunan Kalijaga is held by Prof. Dr. H. Machasin, MA, based on the Decree of the Chancellor of UIN Sunan Kalijaga, Number: 218/Ba.0/A/2005.

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

Starting in 2001/2002 the Postgraduate School of UIN Sunan Kalijaga implemented the Integrated Masters/S3 Curriculum. The system used is full, each student is free to choose the courses offered by fulfilling the predetermined number of credits. Along with the transformation of UIN based on Presidential Decree No. 50 dated June 21, 2004, this institution also changed to the Postgraduate Program of UIN Sunan Kalijaga.