Mogadishu University fosters cooperation with similar institutions for higher education and research; and promotes bilateral and multilateral cooperation with these institutions.
As a result, MU joined a number of national, regional and international higher education organizations.

Mogadishu University is a member of the following organizations:

1. Federation of the Universities of the Islamic World (FUWI).
2. Association of Arab Universities (AARU).
3. The Association of Arab Private Institutions for Higher Education.
4. Islamic Universities League.
5. Association of African Universities.
6. International Universities Council (IUC).
7. Association of international Universities.
8. IGAD Universities League.

List of Partner Universities: Established bilateral links with the following:

1. Europe: Aalborg University, Denmark and Peace Center, University of Toromso, Norway.
2. USA: University of Kansas, USA.
3. Asia: University of Sana, Yemen; University of Aden, Yemen; Open University, Malaysia; Asian University, Malaysia.
4. Africa: (Egypt) University of Halwan, University of Asyut, University of Ain- Shams.
5. (Sudan): University of Khartoum, Omdurman Islamic University, Al- Neelain University, University of Jazeera, Al Zaiem Al Azhari University, International University of Africa, International Institute of Khartoum. (Kenya): Egerton University, (Djibouti) Djibouti University.