Changes in high latitude ocean gateways and CO2 are thought to be main drivers of Cenozoic climate evolution. However, the link between global climate changes and the early ocean gateway formation between the North Atlantic and the Arctic Ocean (incl. the Greenland and Norwegian Seas) controlled by the subsidence of the Greenland-Scotland Ridge is poorly understood. Here, we use a coupled ocean–atmosphere general circulation model for Oligocene-Miocene boundary conditions to address the ventilation history of the Arctic Ocean controlled by the subsidence of the Greenland-Scotland Ridge. Our model simulations reveal that a restricted ocean gateway results in a quiescent Arctic freshwater environment with lagoonal circulation into the North Atlantic. Shallow deepening of the GSR gateway from 22 to 30 and 50 to 100 metres below sea-level forces major reorganizations in the North Atlantic-Arctic circulation induced by a progressive regime shift from restricted lagoonal circulation to a bi-directional flow regime similar to today that is associated with extreme salinity, temperature and sea ice changes in the Arctic Ocean. Taking uncertainties in timing into account this suggests that tectonic processes starting around the Eocene-Oligocene transition may have counterbalanced CO2 induced Arctic cooling by the development of a prototype North Atlantic Current transporting thermohaline waters towards the high northern latitudes.