Initially the campus was located at
Mudende, in Gisenyi prefecture (one component of the current Western Province). The university grew for 10 years until the start of the
Rwandan genocide (April 94 – July 94). During the genocide there was a general breakdown in law and order, and the Mudende campus was looted by the local population, the military, militias, and even AUCA staff before they fled. After the killing stopped, the vacant campus became "a sort of no man's land" for several years and the Mudende campus was stripped of anything removable. At the end of 1996, the campus became a shelter for the first influx of
Zairian refugees from nearby Kibumba (DRC). Although a few months later the Zairian refugees returned home, a larger group of refugees took over the campus, further stripping it of salable items and destroying fixed assets like washrooms.
Conflict during the period of 1997-99 saw additional looting. The university started negotiations with the Rwandan government in 1999 to sell the government the Mudende campus but it was not until 2003 that an agreement was reached. Finally in February 2006 the former campus the Government of Rwanda, represented by its Ministry of Defense, took over the old campus as a base for the
Rwanda Defense Forces. ==Gishushu, Kigali Campus==