The Faculty of Islamic Studies (FDI) was formerly known as the Al-Azhar Special Program, which was established as the implementation of a scientific and cultural cooperation agreement signed on September 17, 1999, in Jakarta, and later revised on March 29, 2002. Although the agreement was signed by the Rector of Al-Azhar University Cairo, Prof. Dr. Ahmad Omar Hashim, and the Rector of Syarif Hidayatullah State Islamic University (UIN) Jakarta, Prof. Dr. Azyumardi Azra, the Ministry of Religious Affairs of the Republic of Indonesia also played an active role as the parent organization for state religious higher education institutions.

The Director of the program was initially appointed as Dr. M. Nursamad Kamba, a lecturer at the Faculty of Ushuluddin at IAIN Bandung. However, a few months later, he was appointed Secretary to the Minister of Religious Affairs, and the responsibility for the program's implementation was handed over to the Assistant Director, Dr. Masri Elmahsyar Bidin, a lecturer at the Faculty of Adab at UIN Syarif Hidayatullah Jakarta.

The inaugural and subsequent lectures were held at the Graduate Program Building of UIN Jakarta, and the Al-Azhar Special Program was attended by 40 students selected from over 300 applicants across various UIN faculties, including Ushuluddin, Sharia, Adab, and Da'wah. Although the program involved several important institutions, it did not run smoothly at first, facing significant internal and external challenges. Some predicted the program would last only a few months and eventually be shut down. However, thanks to the perseverance and determination of various parties, including senior lecturers such as Prof. Dr. Huzaemah T. Yanggo, Prof. Dr. Shalahuddin an-Nadwi, Dr. Anwar Ibrahim, and others, the program was successfully carried out, although the number of students eventually dropped to 27.

As higher education policies evolved, the program's institutional status was deemed no longer relevant and difficult to maintain. Based on this, Prof. Dr. Suwito, as Vice Rector for Academic Affairs, proposed and sought to transform the program into the sixth faculty within UIN. In 2001, this effort succeeded, marked by the issuance of a Rector's Decree formalizing the transformation of the Al-Azhar Special Program into the Faculty of Islamic Studies (FDI), with Dr. Masri Elmahsyar appointed as the first Dean. The FDI structure was then strengthened with the appointment of Dr. M. Syairozi Dimyathi as Vice Dean. Following the transformation of IAIN into UIN Syarif Hidayatullah and the implementation of the new statute in 2003, the FDI leadership structure was expanded with three Assistant Deans: the Assistant Dean for Academic Affairs, held by the former Vice Dean; the Assistant Dean for General Administration, Dr. Amany Burhanuddin Lubis; and the Assistant Dean for Student Affairs, Dr. Ahmad Dardiri.

It is worth noting that FDI’s success and growing popularity are due to its consistent efforts to maintain academic quality by adhering to Al-Azhar University of Egypt's standards for student and faculty recruitment, as well as its curriculum and language of instruction. The recruitment of new students involves an oral exam assessing four Arabic language skills: listening (istima'), reading (qira’ah), speaking (tahaduts), and comprehension (fahm).

Through their studies at FDI, graduates are expected to become practitioners and researchers capable of advancing Islamic studies on a global and competitive scale. This noble goal would be difficult to achieve without the persistence, dedication, and active participation of the entire FDI academic community, including its students.