The academy was established on 1 January 2002. The academy’s first season began in February 2002, as just a place for neighbourhood children to go and play some football. Upon discovering that many of the children actually had talent, the administration formed the various age groups found in the academy today and formed a “Planets” team, which consisted of the best players from these age groups, to represent the club at national and international tournaments.

In 2005, the senior football team was formed with the initiative of former senior team coach, Ibrahim Mbikalo at the insistence of players Karim Rersa, Mohamed Junaid and Azim Butt. On arrival from a tour of the United Kingdom, the team members found themselves overage and with no category to fill in since the youth academy could only accommodate those below fourteen years of age. Under the guidance of Mbikalo, Ligi Ndogo gained their first honours by winning the Private Secondary Schools’ League in 2005, and played in the Kiko Cup towards the end of the year, crashing out through a 3–2 loss to Kibera Combined on penalties.