The Higher Institute of Religious Studies continues the teaching and theological research tradition of the Saint Joseph University of Beirut, which began with the Faculty of Theology, inaugurated in 1881, and traces back to a seminary established in Ghazir in 1846. In 1963, the Institute merged with a religious education program, formally named the "Higher Institute of Religious Formation" (ISFR) in 1970. This institute was created in response to the request of the Council of Major Superiors of Women Religious in Lebanon.

In 1974, when the clergy-specific study program was transferred to the Catholic hierarchy of the Churches of Lebanon, the Faculty of Theology became the Faculty of Religious Studies. Then, in 1980, both the Faculty of Religious Studies and the ISFR, except for the Department of Muslim-Christian Studies, were integrated into the Higher Institute of Religious Studies (ISSR).

In June 2000, a coordinated center for teaching and research in religious studies was established at the Saint Joseph University of Beirut, reviving the Faculty of Religious Studies, and attaching ISSR as an institute within this Faculty. With the new statutes of the Faculty established in February 2009, ISSR, fully integrated, became one of the Faculty’s major components.