At the 8th Summit of IGAD Heads of State held in Khartoum in 2000, IGAD decided to establish a conflict early warning and response mechanism as part of its broader mandate on development, peace and security. The decision also reflected IGAD's realization that timely interventions to prevent escalation or mitigate the worst effects of violent conflicts was more effective and much cheaper than the material and human costs involved when dealing with a full blown crises.

A protocol agreement was signed by the IGAD Council of Ministers on the establishment of CEWARN in January 2002 and in June 2003, the CEWARN Unit was officially opened in Addis Ababa, Ethiopia.