The tropical Pacific and Indian oceans are connected via a complex system of currents known as the Indonesian Throughflow (ITF). The ITF transports mass, heat and freshwater between the two basins, and its impact on the couple climate system depends largely not only on the magnitude of these fluxes, but also on their variability. More than 30% of the variability in the ITF transport has been attributed in the past to the seasonal cycle (Sprintall et al 2009), driven by the reversal of the Monsoon winds. Here we present new estimates of the seasonal cycle of the ITF based on observations of velocity, temperature and salinity in Timor passage collected between 2011 and 2015. These new observations reveal a seasonal cycle with an amplitude larger than previously estimated (approximately 6 Sv from peak to peak). However, the mean Timor throughflow from this period is smaller (4.8 Sv) than existing estimates, in part due to the contribution from the Northwest Shelf, which was previously unaccounted for. The relative contribution from winds, both local and remote, as well as the effect of upstream gating and variability in the source water (North versus South Pacific) are also discussed.