The thermal evolution of Earth is governed by the rate of secular cooling and the amount of radiogenic heating. If mantle heat sources are known, surface heat flow at different times may be used to deduce the efficiency of convective cooling and ultimately the temporal character of plate tectonics. We estimate global heat flow from 65 Ma to the present using seafloor age reconstructions and a modified half-space cooling model, and we find that heat flow has decreased by similar to 0.15% every million years during the Cenozoic. By examining geometric trends in plate reconstructions since 120 Ma, we show that the reduction in heat flow is due to a decrease in the area of ridge-proximal oceanic crust. Even accounting for uncertainties in plate reconstructions, the rate of heat flow decrease is an order of magnitude faster than estimates based on smooth, parameterized cooling models. This implies that heat flow experiences short-term fluctuations associated with plate tectonic cyclicity. Continental separation does not appear to directly control convective wavelengths, but rather indirectly affects how oceanic plate systems adjust to accommodate global heat transport. Given that today’s heat flow may be unusually low, secular cooling rates estimated from present-day values will tend to underestimate the average cooling rate. Thus, a mechanism that causes less efficient tectonic heat transport at higher temperatures may be required to prevent an unreasonably hot mantle in the recent past.