The origins of the Ushuluddin Faculty at UIN Syarif Hidayatullah Jakarta began with the Department of Da'wah wal Irsyad which was founded in 1959 during the ADIA era. This department is also known as the Special Department, because its students consist of army priests who are given the task of studying, both Army (AD) and Air Force (AU) soldiers. In 1960, this department was known as PT-PAL (Navy Officer Tjalon Education) because the students came from the Navy. At the time of the merger of ADIA Jakarta and PTAIN Yogyakarta to become IAIN Al-Jami'ah, this Special Department was included in the Tarbiyah Faculty of IAIN Jakarta Branch. However, its existence at the Tarbiyah Faculty did not last long, because in 1961, in order to complement the existing faculties at the IAIN Jakarta Branch, it was decided to open the Ushuluddin Faculty. Initial implementation began with the opening of new classes in the 1962 Academic Year. Furthermore, based on the Decree of the Minister of Religion of the Republic of Indonesia No. 66 of 1962 On November 5 1962, the Jakarta Branch of the Ushuluddin Faculty of IAIN was declared officially established. In 1964 the Ushuluddin Faculty opened a Da'wah Department for undergraduate level (S1). This Da'wah Department issued its alumni (Complete Bachelors) for the first time in 1968. In 1967 the Ushuluddin Faculty established the Department of Comparative Religion (now Religious Studies) at undergraduate level (S1), and 3 years later this department graduated its undergraduates. In 1982, the Faculty, which is known as a hotbed for critical thinkers, opened the Department of Aqidah Philosophy (now Aqidah and Islamic Philosophy). With the establishment of this department, the image of the Ushuluddin Faculty as a faculty that supports the renewal of Islamic thought in Indonesia has become stronger.

In 1989 IAIN Jakarta inaugurated the establishment of the Da'wah Faculty. This faculty accepted new students starting in the 1989/1990 academic year, while students who had registered in the Da'wah Department at the Ushuluddin Faculty continued to complete their education at the Ushuluddin Faculty. As a replacement for the Da'wah Department, in the 1989/1990 academic year the Ushuluddin Faculty also established the Hadith Tafsir Department. When reform rolled around in this country.

In the 1999/2000 academic year, the Ushuluddin Faculty opened two new study programs at once: the Sociology of Religion Study Program and the Islamic Political Thought Study Program. It is hoped that from these two study programs a discourse of integration between religious (Islamic) sciences and empirical social sciences will emerge and develop. Thus, the Ushuluddin faculty has 5 departments or study programs, namely Comparative Religion (1967), Aqidah and Philosophy (1982), Tafsir Hadith (1989), Sociology of Religion (1999) and Islamic Political Thought (1999). In accordance with the Decree of the Chancellor of UIN Syarif Hidayatullah Jakarta Number: 477 of 2016 concerning Adjustments to the Nomenclature of Study Programs at the Faculty of Ushuluddin UIN Syarif Hidayatullah Jakarta that the Department of Tafsir Hadith (TH) and Aqidah Philosophy (AF) should no longer be used, the leadership of the Faculty of Ushuluddin in 2015 decided that the Hadith Tafsir Department of UIN Syarif Hidayatullah Jakarta changed its name to the Department of Al-Qur'an and Tafsir Science (IAT) which was confirmed by the Request of the Chancellor of the Syarif Hidayatullah State Islamic University Jakarta Number: Un.01/R/OT.00.1/580/2015 dated March 16 2015 concerning Adjustment of the Nomenclature of the Hadith Tafsir Study Program to Al-Qur'an and Tafsir Science (IAT) and Hadith Science (IH), Philosophy Aqidah to Islamic Aqidah and Philosophy (AFI) and Sufism Science (IT), which then issued a Decree Director General of Islamic Education Number: 3252 of 2015 concerning Adjustments to the Nomenclature of Study Programs at UIN Syarif Hidayatullah Jakarta in 2015