Sultan Agung Islamic University, or Unissula, was founded by the Sultan Agung Waqf Foundation (YBWSA) on the 16th of Dzulhijjah 1381 AH, which corresponds to May 20, 1962 AD. The name Sultan Agung is taken from Sultan Agung, a national hero who rendered significant services to the Indonesian nation. Sultan Agung's full name was Adi Prabu Hanyokrokusumo, who was born in Kotagede, Mataram Sultanate, in 1593. Sultan Agung was the third sultan of the Mataram Sultanate, ruling from 1613–1645. Under his leadership, the Mataram Sultanate developed into the largest kingdom in Java and the Indonesian archipelago at the time.

The choice of Sultan Agung as the university's name was also influenced by various considerations, including his being a great leader who deeply loved his nation and country and was very persistent in resisting various colonial forces. Sultan Agung was a religious king with a superior character who was able to implement religious life through cultural acculturation that was accepted by the community. Therefore, it is not surprising that his services as a fighter and cultural figure led to Sultan Agung's being designated as a national hero of Indonesia based on Presidential Decree No. 106/TK/1975 dated November 3, 1975.

This rationale makes it logical to name Sultan Agung as the university's name, and it is hoped that this name will continue to ignite the spirit of struggle to build the nation through education with Islamic values.

Today, at over 60 years old, Unissula has grown into a leading university in Indonesia with an UNGGUL accreditation rating from BAN-PT, with 13 faculties and 45 study programs consisting of D3, S1, S2, and S3 degrees.