Assessing temporal variability in extreme rainfall events before the historical era is complicated by the sparsity of long-term "direct" storm proxies. Here we present a 2,200-y-long, accurate, and precisely dated record of cave flooding events from the northwest Australian tropics that we interpret, based on an integrated analysis of meteorological data and sediment layers within stalagmites, as representing a proxy for extreme rainfall events derived primarily from tropical cyclones (TCs) and secondarily from the regional summer monsoon. This time series reveals substantial multicentennial variability in extreme rainfall, with elevated occurrence rates characterizing the twentieth century, 850-1450 CE (Common Era), and 50-400 CE; reduced activity marks 1450-1650 CE and 500-850 CE. These trends are similar to reconstructed numbers of TCs in the North Atlantic and Caribbean basins, and they form temporal and spatial patterns best explained by secular changes in the dominant mode of the El Niño/Southern Oscillation (ENSO), the primary driver of modern TC variability. We thus attribute long-term shifts in cyclogenesis in both the central Australian and North Atlantic sectors over the past two millennia to entrenched El Niño or La Niña states of the tropical Pacific. The influence of ENSO on monsoon precipitation in this region of northwest Australia is muted, but ENSO-driven changes to the monsoon may have complemented changes to TC activity.