The history of the Arctic Ocean during the Cenozoic era (0–65 million years ago) is largely unknown from direct evidence. Here we present a Cenozoic palaeoceanographic record constructed from >400 m of sediment core from a recent drilling expedition to the Lomonosov ridge in the Arctic Ocean. Our record shows a palaeoenvironmental transition from a warm ‘greenhouse’ world, during the late Palaeocene and early Eocene epochs, to a colder ‘icehouse’ world influenced by sea ice and icebergs from the middle Eocene epoch to the present. For the most recent ∼14 Myr, we find sedimentation rates of 1–2 cm per thousand years, in stark contrast to the substantially lower rates proposed in earlier studies; this record of the Neogene reveals cooling of the Arctic that was synchronous with the expansion of Greenland ice (∼3.2 Myr ago) and East Antarctic ice (∼14 Myr ago). We find evidence for the first occurrence of ice-rafted debris in the middle Eocene epoch (∼45 Myr ago), some 35 Myr earlier than previously thought; fresh surface waters were present at ∼49 Myr ago, before the onset of ice-rafted debris. Also, the temperatures of surface waters during the Palaeocene/Eocene thermal maximum (∼55 Myr ago) appear to have been substantially warmer than previously estimated. The revised timing of the earliest Arctic cooling events coincides with those from Antarctica, supporting arguments for bipolar symmetry in climate change.