In February 1988, the university's founder His Beatitude Patriarch Ignatius IV, the Patriarch of the Greek Orthodox Church of Antioch and all the East, defined what he believed would be the present Orthodoxy has to offer to both Christians and Muslims alike: a university that serves as the beacon of learning, of love, and of tolerance that emanates from the very core of the Orthodox theology.

The Patriarch chose to place the university on a plot by the historic Monastery of Balamand, founded by the Cistercian monks in the 12th century. His choice comes as no surprise given the monastery's long heritage of being a center of learning in North Lebanon during the 19th century and home to the first printing press in Lebanon. It also offered ample space to build a campus that is situated conveniently on a spectacular hill some 10 kilometers south of Tripoli, one kilometer east of the Mediterranean Sea, and 70 kilometers north of Beirut.

With no other university in North Lebanon and a pledge of 480,000 m2 of land, The University of Balamand would answer a pressing local need to its surrounding community. It opened its doors with three faculties to a few hundred students and a handful of professors. Two of them existed before as independent entities, namely the Saint John of Damascus Institute of Theology (founded in 1970) and the Lebanese Academy of Fine Arts (ALBA, founded in 1936). A third, the Faculty of Arts and Social Sciences was created to meet the stipulations of Lebanese law.

The same year, the Patriarch appointed a board of trustees, who were drawn to The University of Balamand by the idea of a community of great scholars. The board who is the highest governing authority at the university, elected Dr. George Tomeh, a philosopher, a diplomat, and professor at the American University of Beirut, as the first president.

In 1990, the leading Lebanese statesman and journalist, Mr. Ghassan Tueini succeeded Dr. Tomeh. Mr. Tueini took on the management of the university in addition to his responsibilities as publisher of the al-Nahar Newspaper. By 1993, the Board appointed Dr. Elie A. Salem as a full-time president who would preside at the university's main campus and assumes full responsibility for its further growth. Dr. Salem diligently served the university for the next consecutive 25 years (1993-2018) and was succeeded in October 2018 by Dr. Elias Warrak.

In 2004, the university adopted a Master plan prepared by the Sasaki Corporation of Boston and in 2010 approved an ambitious Strategic Plan 2010-2020 which is still undergoing implementation.

Today, the university's main campus remains on the Balamand Hill with four campuses across Lebanon. The University is also in the process of constructing a new hospital under the name of University of Balamand Medical Center.