ISSEA was created in 1998 through the initiative of original member schools: American International School of Johannesburg, Harare International School, International Community School of Addis Ababa, International School of Kenya, International School of Tanganyika and International School of Uganda. It was established as a sports conference sponsoring basketball, soccer, and volleyball.
In 2010 the American International School of Lusaka joined. In 2013 the American International School of Mozambique also joined.
In 2014 sports tournaments included golf, rugby, soccer, swimming, track and field/cross country, and tennis.
In addition to sports events, the organisation expanded to sponsor cultural conventions in band, choir, drama, and visual arts.
From its origins as a math competition, a Science, Technology, Engineering, and Mathematics (STEM) festival began in 2016.