South East Europe is an area that has lived through many changes in recent history. Combining considerable political and social changes in Eastern Europe, added to even more recent armed conflicts in the former Socialist Federal Republic of Yugoslavia, the map of this region has changed considerably. SFRJ having fallen apart, new countries emerged in the early 1990's including Republic of Slovenia, Republic of Croatia, Bosnia and Herzegovina with two entities (Federation of Bosnia and Herzegovina and Republic of Srpska) Republic of Macedonia, Republic of Montenegro and the Republic of Serbia. Most of these countries are now part of SEPCA added to Romania, Republic of Bulgaria and Republic of Albania.

Armed conflicts in the region and the dismantling of the former SFR Yugoslavia resulted in many casualties. In these times police officers carried out mostly military tasks instead of their regular police duties. Considerable historical and social changes caused the restructuring of the police services and their adaptation to the changes and the new challenges.

At the beginning of SEPCA initiative, The Canadian Government, in a joint venture between the Canadian International Development Agency and the Royal Canadian Mounted Police have greatly assisted member countries in the establishment of the Southeast Europe Police Chiefs Association. Its objectives were and are to improve police cooperation between members, develop professionalism and facilitate reforms in the police services.

SEPCA was formed in Pula, Republic of Croatia in January 2002. The Statute of the association was adopted in October 2002 in Bucharest, Romania. At that same time the Executive Board and management of the association were elected. The Association held its first official Annual general meeting on June 2003, in Belgrade, Serbia being at this time the site of its Secretariat office.

After signing the new SEPCA statutes in 2007, the association built partnerships with the Swiss Agency for Development and Co-ordination (SDC) and the Geneva Centre for the Democratic Control of Armed Forces (DCAF) and with other institutions that the association would focus on regional strategy building in public security and on projects implementation. The National Directors of Police approved a joint vision on future SEPCA activities which vision is the basis of the 3-Year strategy. This vision offers to cooperate with all regional partners streamlining all activities in order to build public security and best cross-border police co-operation.