At the time of its establishment in 1982, the Postgraduate Studies had only one department with the emphasis on Islamic studies. In the academic year of 1996/1997 I another department, i.e. Shari'a was opened, and in the following academic year ( 1997/1998) four other departments were initiated. They were: Islamic Thought, Tafsir and Hadith, Islamic History and Civilization and Islam and Modernity.

In addition to the master and doctorate programs conducted through regular classes, a program called "Doctor by Research" has also been introduced. The Post-graduate Studies of UIN Jakarta has also opened an international class using Arabic and English as the media of instruction.

In the academic year of 2002/2003, The Postgraduate Studies has the following departments with eight different specialties:

1. Islamic Thought

This Department graduates scholars with the qualification of master and doctorate degrees in the fields of theology, philosophy, and Sufism.

2. Shari'a

This Department graduates scholars with the qualification of master and doctorate degrees in the field of Shari'a.

3. Islamic Education

This Department graduates scholars with the qualification of master and doctorate degrees in the field of Islamic education.

4. Islamic History and Civilization

This Department graduates scholars to attain their master and doctorate degrees in the fields of Islamic history and civilization.

5. Tafsir and Hadith

This Department graduates scholars with the qualification of master and doctorate degrees in the fields of Quranic exegesis and Prophetic traditions.

6. Arabic Language and Literature

This Department graduates scholars with the qualification of master and doctorate degrees in the fields of Arabic language and literature.

7. Da'wa and Communication

This Department graduates scholars with the qualification of master and doctorate degrees in the fields of da'wa and communication.