Modern precipitation over northeastern (NE) South America is strongly controlled by the seasonal meridional migration of the Intertropical Convergence Zone (ITCZ). Ample evidence from the Northern Hemisphere suggests a mid- to late Holocene southward migration of the ITCZ. Such a shift would be expected to increase precipitation over semi-arid northern NE Brazil (Southern Hemisphere). However, the most robust precipitation record from northern NE Brazil shows a drying trend throughout the Holocene. Here, we address this issue presenting a high-temporal resolution reconstruction of precipitation over northern NE Brazil based on data from a marine sediment core, together with analyses of mid- and late Holocene simulations performed with the fully coupled climate model FGOALS-s2. Both, our data and the climate model simulations show a decrease in precipitation over northern NE Brazil from the mid- to the late Holocene. The model outputs further indicate a latitudinal contraction of the seasonal migration range of the ITCZ that, together with an intensification of the regional Walker circulation, were responsible for the mid- to late Holocene changes in precipitation over NE South America. Our results reconcile apparently conflicting precipitation records and climate mechanisms used to explain changes in precipitation over NE South America.