CAFF was established in 1991 to address the conservation of Arctic biodiversity in a rapidly developing region.

CAFF formed one of four program areas of The Arctic Environmental Protection Strategy (AEPS), which was adopted by Canada, the Kingdom of Denmark, Finland, Iceland, Norway, the Russian Federation, Sweden and the United States through Ministerial Declaration at Rovaniemi, Finland (often referred to as "the Rovaniemi Process").

Since its inagual meeting in Ottawa, Canada in 1992, CAFF has provided scientists, conservation managers, governments and Indigenous Peoples with a forum in which to tackle a wide range of Arctic conservation issues at the circumpolar level.

When the Arctic Council was established in 1996, CAFF became one of the Council's Working Groups. The Arctic Council is the leading intergovernmental forum promoting cooperation, coordination and interaction among the Arctic States, Arctic Indigenous peoples and other Arctic inhabitants on common Arctic issues, in particular on issues of sustainable development and environmental protection in the Arctic.