Lake Petén Itzá, Guatemala, is one of the oldest lakes in northern Central America. Its sedimentary record contains the signal in precipitation variability of the last four interglacial-glacial cycles (420-14 cal ka BP). Changes in rainfall during the last 80 kyr have been widely described in the lake’s record and associated with shifts in the Intertropical Convergence Zone (ITCZ) and the Atlantic Meridional Oceanic Circulation (AMOC). However, there is limited knowledge regarding the hydrological responses of Petén Itzá prior to this time interval due to a poorly constrained chronology. Here, we provide a significantly improved chronology allowing a more detailed analysis of changes in runoff, evaporation, and vegetation throughout the last 420 kyr. Magnetic susceptibility, bulk density, elemental geochemistry and pollen data indicate that glacial periods were characterized by dry conditions, generally associated with low runoff, high evaporation and temperate environments. On the contrary, interglacial periods suggest wetter conditions with high runoff, low evaporation and dominance of tropical vegetation. Our results are consistent with other paleo-precipitation records in the region, such as the marine records ODP 1239 from the eastern equatorial Pacific and the ODP 1002 from Cariaco Basin, suggesting that the runoff variability at Petén Itzá may be associated with the long-term latitudinal migration of the ITCZ. Frequency analyses of our data show the presence of 100, 40 and 21 kyr periodicities and thus an orbital control. Our study serves as a first reference point in the transregional study of the late Quaternary climate in northern Central America.