Presented here are stable nitrogen isotope data from a rock hyrax (Procavia capensis) middens from northwestern Namibia that record a series of rapid aridification events beginning at ca. 3800 cal yr BP, and which mark a progressive decrease in regional humidity across the Holocene. Strong correlations exist between this record and other terrestrial and marine archives from southern Africa, indicating that the observed pattern of climate change is regionally coherent. Combined, these data indicate hemispheric synchrony in tropical African climate change during the Holocene, with similar trends characterising the termination of the ‘African Humid Period’ (AHP) in both the northern and southern tropics. These findings run counter to the widely accepted model of direct low-latitude insolation forcing, which requires an anti-phase relationship to exist between the hemispheres. The combined dataset highlights: 1) the importance of forcing mechanisms influencing the high northern latitudes in effecting low-latitude climate change in Africa, and 2) the potential importance of solar forcing and variations in the Earth's geomagnetic shield in determining both long-term and rapid centennial-scale climate changes, identifying a possible mechanism for the variations marking the AHP termination in both the southern and northern tropics.