Eastern Africa continues to be confronted with serious terrorism threats. As the sustained terrorist activity aims to destabilize governments and undermines economic and social development, strong coordination and cooperation within national governments and between states and organizations at the regional and international level, in sharing best practices and lessons learned as well as assisting with investigation and prosecution of terrorism cases, is essential to effectively combat terrorism. Support for, and radicalisation and recruitment into, terrorist organisations is predicted to increase if counter strategies and measures are not well organized and clearly defined while demonstrating respect for human rights and the rule of law. This emphasizes the need to promote and support a comprehensive response including strengthening the legal framework, building the technical and operational capacity of law enforcement officials and public prosecutors and enhancing regional and international cooperation to prevent and counter terrorism.

In response to the persisting threats and needs identified by Member States in Eastern Africa, the Council of Police Chiefs (CPC) of the Eastern African Police Chief Cooperation Organization (EAPCCO) in 2012 recommended the establishment of the EAPCCO CTCoE with a focus on timely sharing of information; coordinated planning and action, and sharing of experiences and best practices among member states. Hence, in 2018, EAPCCO adopted a resolution creating the EAPCCO CTCoE, which was established and housed at the Directorate for Criminal Investigation (DCI) Headquarters in Nairobi, Kenya. The Government of Kenya sponsored the appointment of the director, Mr. Sospeter Munyi, of the CTCoE while the Government of Uganda seconded a senior officer, Mr. John Ndungutse (former commander of its counter-terrorism unit) to the CTCoE to help establish the CTCoE. The INTERPOL Regional Bureau (RB) for Eastern Africa currently provides administrative support to the CTCoE as Secretariat to EAPCCO.

During the 22nd EAPCCO Annual General Meeting (AGM), held virtually in September 2020, Police Chiefs at the meeting reaffirmed their commitment to support the success of the CTCoE.