The history of the UNAM Football Club dates back to the late 1990s when the club was composed merely of students that took part in the UNAM Home League. The home league consisted of 16 football clubs with students from Polytechnic, former Windhoek College of Education (currently known as Khomasdal Campus), Neudamm Campus and UNAM Main Campus. In 2002/2003, the team was crowned as the Khomas Second Division League champions and promoted to the Nation Wide First Division League under the leadership of Coach Willem Kapukare. In the 2004/2005 soccer season, the UNAM Football Club was awarded a silver medal (2nd place).
Due to the restructuring of national leagues, UNAM FC could unfortunately not participate in the promotion / relegation play-offs in order to remain in the Nationwide 1st Division. This led the team to be relegated to the Khomas Second Division League. In 2007/2008 soccer season, the team was once again crowned champions of the Khomas Second Division and promoted to the Southern Stream First Division League. Since its inception, the club produced top quality players that moved to Premier League clubs is search for exposure.
To a certain extent, this has negatively affected the development and progress of UNAM FC because it could not produce players for itself but rather for Premier League clubs due to other benefits. To date, the UNAM Football Club, can pride itself by acknowledging that it has significantly contributed to football development in the Land of the Brave and with the opportunity bestowed on it to partake in the Namibian Premier League, more can be achieved.