Balkan Civil Society Development Network was established based on initiative Capacity Building Hub Programme, a part of a larger initiative called the WCC South-East Europe Ecumenical Partnership. By bringing together churches, ecumenical and civil society organizations, this initiative aimed at promoting their co-ordination and co-operation. The Capacity-Building Hub Programme implemented by the Macedonian Center for International Cooperation (MCIC) focused on strengthening individual/staff and organizational capacities and skills of involved agencies.

The initial pilot programme ran from 2001 to 2003, in which 5 country visits and accompanying reports, 3 partnership meetings, 5 trainings, 7 exchange and consultancy visits were held and web training-directory and addressbook were published. Thus, Balkan Civil Society Development Network was launched as an informal network in December 2003. The network held its Founding assembly on 6th July, 2009 in Skopje, Macedonia and is a legaly registered organization since 30th September, 2009.