Named after Israeli national founder David Ben-Gurion, the university was founded in 1969 and currently has five campuses: three in Beersheba, one in Sede Boqer and one in Eilat.

The University was later renamed after Israel's founder and first prime minister, David Ben-Gurion, who believed that the future of the country lay in this region.

The Presidents of the university have been Moshe Prywes (1973–75), Yosef Tekoah (1975–81), Shlomo Gazit (1982–85), Chaim Elata (1985–90), Avishay Braverman (1990–2006), Rivka Carmi (2006–18), and Daniel Chamovitz (2019–present).

[7] In 2016, the late Dr. Howard and Lottie Marcus bequeathed a legacy gift of approximately $400 million to Ben-Gurion University.

In 1978 Prof. Alfred Inselberg, then with the Faculty of Mathematics, together with Dr. Sam Bergman and Dr. Avraham Melkman initiated the Computer Science program which by 1982 had attracted more than 200 students.

In October 2018, The Medical School for International Health celebrated 20 years of existence, by holding a two-day seminar to recognize its achievements and bring together its many partners from around the world.

For the first time in the program's history, the faculty presented each student of the class with an actual White Coat emblazoned with the MSIH logo.