The Indonesian Throughflow (ITF), as the sole low-latitude conduit connecting the Pacific and Indian Oceans, regulates the thermohaline balance between these oceans. Investigating the spatio-temporal variability of the ITF and its relationship to precessional forcing is, thus, crucial for understanding the drivers of tropical climate change. Here, we reconstruct the history of the ITF over the past ~120 kyr, based on high resolution (~400 yr) δ18O and Mg/Ca records of Globigerinoides ruber and Pulleniatina obliquiloculata from Core SO217-18540 retrieved from the Flores Sea upwelling region within the main pathway of the ITF. Comparison of these new records with published paleo-oceanographic and climatological data from the western tropical Pacific suggests that annual mean conditions in the Flores Sea were controlled by the ITF rather than by monsoonal upwelling. Our results further indicate that precessional insolation was a major forcing for the hydrological evolution of the ITF during the past 120 kyr. We suggest that precessional insolation forcing paced ITF variability by modulating the mean state of El Niño-Southern Oscillation-like conditions and latitudinal shifts or expansion/contraction of the Intertropical Convergence Zone.