The African and Arab Youth Council was founded in 2004 at the conclusion of the international youth festivals for the African and Arab Youth in Khartoum, under the auspices of the President of Sudan and Libya. Consequently, in 2005, an Executive Committee was formed for Organization to follow and fulfill the aspiration of the youth of the Africa & Arab World. The executive followed up the legal mandate and membership of the Organization especially with African Union and Arab League.

By consensus, a decision was taken that the Secretariat be housed in Khartoum, Sudan, with the generous support of the Government of Sudan until 2008 when a new decision was taken during the Afro Arab Youth festival in Kampala. At the conclusion of the AAYF 2008, two fundamental decisions were taken among others; that the Afro Arab Youth Headquarter be constructed in Uganda, this was unanimously agreed upon by H:E Muammar Gaddafi of Libya and the two presidents who were present on that day offered land and other resources for this cause.

Patronship of the Organization now went to the host President of Uganda H.E Y.K Museveni who offered a prime land for the construction of the headquarters which was initiated with an offer of the prime land for this exercise by H.E YK Museveni the President of the Republic of Uganda.  Several meetings for both the Executive and General Assembly have been taking place since 2004 to date in different parts of the member states including Khartoum, Damascus, Cairo, Kampala, Rabat, Casablanca, Tripoli, Qatar, etc. These have taken various decisions to all of which carries among the legal directives of Afro Arab youth Council.