An observed decline in the Eastern African Long Rains from the 1980s to late 2000s appears contrary to the projected increase under future climate change. This “Eastern African climate paradox” confounds use of climate projections for adaptation planning across Eastern Africa. Here we show the decline corresponds to a later onset and earlier cessation of the long rains, with a similar seasonal maximum in area-averaged daily rainfall. Previous studies have explored the role of remote teleconnections, but those mechanisms do not sufficiently explain the decline or the newly identified change in seasonality. Using a large ensemble of observations, reanalyses and atmospheric simulations, we propose a regional mechanism that explains both the observed decline and the recent partial recovery. A decrease in surface pressure over Arabia and warmer north Arabian Sea is associated with enhanced southerlies and an earlier cessation of the long rains. This is supported by a similar signal in surface pressure in many atmosphere-only models giving lower May rainfall and an earlier cessation. Anomalously warm seas south of Eastern Africa delay the northward movement of the tropical rain-band, giving a later onset. These results are key in understanding the paradox. It is now a priority to establish the balance of mechanisms that have led to these trends, which are partially captured in atmosphere-only simulations.