Today's cryosphere reflects an extreme climate state that developed through stepwise global Cenozoic cooling. In this context the opening of the Fram Strait, the Atlantic-Arctic Gateway (AAG), enabled deep-water exchange between the northern North Atlantic and the Arctic Ocean and thereby influenced global ocean circulation and climate. Here we present a new age model for Ocean Drilling Program Site 909 located in the Molloy Basin, a key site to investigate the late opening phase of the central Fram Strait and the early history of oceanic circulation in the AAG. Our results are based on a revised magnetostratigraphy calibrated by new palynomorph bioevents, which shifts previously used stratigraphies for Site 909 to significantly younger ages in the time interval from c. 15 Ma to 3 Ma. The revised late Miocene to present chronology combined with an improved core-log-seismic integration leads to a new high-resolution seismic stratigraphy for the central Fram Strait that allows a more comprehensive correlation with seismic markers from the western Barents Sea margin and also the adjacent Yermak Plateau. The new stratigraphy implies that prominent maxima in coarse sand particles and kaolinite, often interpreted as evidence for ice rafting in the Fram Strait occur at c. 10.8 Ma, c. 3 Myr later as previously inferred and thus well after the Middle Miocene Climate Transition (c. 15–13 Ma). In the late Tortonian (<7.5 Ma), sediment transport became current controlled, mainly through a western, recirculating branch of the West Spitsbergen Current. This transport was strongly enhanced between c. 6.4 and 4.6 Ma and likely linked to the subsiding Hovgaard (Hovgård) Ridge and the widening of the AAG. Late Pliocene to Pleistocene seismic reflectors correlate with episodes of elevated ice-rafted detritus input related to major steps in Northern Hemisphere ice sheet growth such as the prominent glacial inception MIS M2 that predates the mid-Piacenzian Warm Period and the intensification of Northern Hemisphere glaciation starting at c. 2.7 Ma. At the beginning of the Mid Pleistocene Transition (c. 1.2–0.8 Ma), sediment accumulation in the Fram Strait significantly decreased.