Since the Kvarken as the narrowest part ot the Gulf of Bothnia united Ostrobothnia (Österbotten) and Västerbotten people in the early days learned how to cooperate. In the 14th century the northern part of Sweden was ruled from the Korsholm Castle in Ostrobothnia. For a long time the people who were living on the islands Björkö and Holmön transported mail and passengers over the Kvarken, a predecessor of the Kvarken traffic and the Kvarken cooperation of today. In a map from 1539 shows how the Kvarken was drawn and how transport over the Kvarken was handled in different seasons.

Map: Olaus Magnus, Carta Marina Scandinavia, 1539 (excerpt)

In the 1830ies the first steamship lines started in the Gulf of Bothnia and in the Kvarken. The traffic has from time to time became more regular. In 1958 the first car ferry came and from 1972 the has been traffic all year round.

A more organised cooperation in the Kvarken Region grew from the Nordic Cooperation. The associations Pohjola-Norden in Finland and Föreningen Norden in Sweden as well as from the twinning of towns and municipalities.

The Kvarken Council was started in 1972 at the first Kvarken Conference in Vasa: In the first years the organisation was formed and the work was started. In 1979 The Kvarken Council became a part of the official Nordic cooperation, with a financial support from the Council of Nordic Ministers.