Growth lines in the mineralized tissues of living and fossil organisms often exhibit regular patterns that record daily, monthly, or annual cycles. Growth laminations in fossil corals and other marine invertebrates indicate long-term deceleration of the Earth’s rotation, probably largely due to tidal friction, resulting in a decline in the number of days per year over the Earth’s history. Fossils suggest the rate of decline has not been uniform, with the trend between the late Carboniferous and Cretaceous in particular departing from preceding and subsequent periods. However, insufficient data have obscured the nature and cause of the apparent halt in despinning within this time interval. Here we present new fossil geochronometer data that reveal a sustained acceleration in the Earth’s rotation in the early Mesozoic Era, lasting about 90 million years and producing a decrease in the length of day (LOD) at an average rate of about 3 ms/cy. The coincidence of this acceleration with certain geophysical events including the final assembly of Pangaea and a change in the intensity and stability of the geomagnetic field strongly suggests that its cause is rooted in the deep interior of the Earth. A similar explanation has been proposed for observed decadal variations in the Earth’s rotation. Our results suggest large-scale linkage of rotational variation, tectonics, and the geomagnetic field to core–mantle boundary (CMB) dynamics. Furthermore the newly identified acceleration in the Earth’s rotation which began at the end of the Paleozoic, and the geophysical factors that are associated with it, can ultimately bear on the causal mechanisms behind the Permo-Triassic mass extinction.