The educational as well as all other public service institutions disappeared after the central government collapsed in 1991. The civil unrest that followed almost destroyed the educational infrastructure, subsequently all educational institutions whether primary, secondary and tertiary institutions totally ceased to function.
After many years later, private indigenous schools started in many parts of the country. Puntland known then as the North Eastern Regions was not an exception. In most of the major towns and in many districts and counties small scale primary schools sprung up. The outputs of these indigenous schools compelled the need to create high schools.

Many high schools were started in the same basis as their primary schools. The graduates of high schools increased in number and required to continue their education. Some of those students whose families could afford to cover their educational expenses were sent to Asian countries like India and Pakistan and Malaysia . Some others found scholarships from Arab countries like Egypt and Sudan . But most of these high school graduates needed local tertiary educational institution that could fill the educational gap, and offer educational facilities not only to the current school graduates but also provide new opportunities for those whose faculties have been in the disappeared Somali National University to complete their studies.

The establishment of East Africa University (EAU) of Bosaso came to fill this important gap in the stateless educational system of Somalia and as response to the peoples need by bringing different provision of skills and training the youth in order to participate in the development of their country. This could be regarded as an instrumental institution for expanding the educational system in order to graduate qualified people capable of meeting the needs of the country's ambitious future development plans.

However, East Africa University has opened its door to accommodate high school graduates in Puntland in October 1999. Early 2000 the university received its first intake of students and delivered pre-university courses for the students. This course offered the students a basic and minimum knowledge of Applied Mathematics, Communication skills in both English and Arabic. After a period of six months study (1st October 2000), the students were evaluated and selected to the two faculties existed that time, Faculty of Business Administration and Faculty of Shari'a and Islamic Studies. Since then, the university was growing and developing gradually until it has started to expand to other regions.

The main campus of East Africa University (EAU) is located at the city of Bosaso , Puntland State of Somalia . This campus of the university in Bosaso occupies 49.19 hectares of land and it is built on different blocks. Bosaso site was chosen for university main campus on the grounds of its large metropolitan population, numerous secondary schools and the commercial importance. The first expansion branch campus was built at Galkayo City of Mudug region for the Faculty of Education and the Institutes of IT and Nursing. The first intake of students was September 2006.