Heliopolis University was established by presidential decree 298/2009 in 2009.
In 2012 the first 128 students enrolled in the faculties of Business and Economics, Engineering and Pharmacy.

The idea to create a sustainable university was developed by Ibrahim Abouleish, the leader of the SEKEM initiative, which was founded in 1977. In his vision the university is an important part in the SEKEM Initiative. Like other parts of SEKEM, the University follows sustainable principles. These principles are divided in different dimensions, like societal, cultural, and business life, which have to go hand in hand with the environment. The SEKEM Initiative handled these four main dimensions in a specific framework, which called sustainable flower.

Based on this framework, students not only learn their specific curricula, but also take lessons in arts, culture, social sciences, environmental studies, and foreign languages. These skills are handled in an obligatory study which is called Core program. For teaching purposes and to promote sustainability, Heliopolis University operates a wastewater system and several photovoltaic installations, students and staff can use a cafeteria, a restaurant, as well as sport and leisure facilities. Furthermore a botanical garden is integrated in the campus of the University.