Intercooperation was created in 1982 at the initiative of the Swiss Development Agency, SDC. Until 1997, Intercooperation existed as an association of seven Swiss development NGOs. In those years, Intercooperation received from SDC a range of projects in the domain of rural development for execution. Most projects were in the fields of forestry, agriculture, in particular livestock development, NGO-support and financial services. Priority countries since the beginning were India, Pakistan, Rwanda, Madagascar, Tanzania, Mali, Peru and Bolivia. In India, Pakistan and Madagascar, SDC entrusted Intercooperation with programme mandates for the entire natural resources management sector.

In the mid-nineties, SDC started competitive bidding processes for project execution mandates. The relationship of Intercooperation with SDC became more business-like. In a more difficult financial context, elements of competition developed between NGOs. Intercooperation hence changed to a new legal status and became in 1997 a foundation under Swiss law with a broadened range of membership of 21 organisations, only 4 of them being development NGOs.

In the nineties, Intercooperation slowly began to accept new mandates othe than from SDC. Long-term mandates were established with seco, the Swiss State Secretariate for Economic Affairs, ITTO, the International Tropical Timber Organisation, and others. Short term consultancies were conducted on behalf of the World Bank, IFAD, GtZ, the Austrian Development Agency etc. Project funds were received from the Dutch, the Canton Vaud and after 2000 from the EU and other donors.

The important Rwanda programme collapsed in 1994 at the time of the genocide. New programmes with SDC developed mainly in Central Asia and Eastern Europe, but also in Central America, Bangladesh and Tunisia. After 2000, IC's range of thematic competence expanded towards small enterprise promotion, market development of agricultural and forestry products, decentralization and municipal development and questions related to climate change and environmental services.

In 2004, Intercooperation is legally a completely autonomous organisation with still very strong business links to SDC and a policy of further broadening its financial base. Intercooperation does not engage in public fund-raising.