The El Niño/Southern Oscillation (ENSO) drives substantial variability in tropical cyclone (TC) activity around the world1, 2, 3. However, it remains uncertain how the projected future changes in ENSO under greenhouse warming4, 5, 6, 7, 8 will affect TC activity, apart from an expectation that the overall frequency of TCs is likely to decrease for most ocean basins9, 10, 11. Here we show robust changes in ENSO-driven variability in TC occurrence by the late twenty-first century. In particular, we show that TCs become more frequent (~20–40%) during future-climate El Niño events compared with present-climate El Niño events—and less frequent during future-climate La Niña events—around a group of small island nations (for example, Fiji, Vanuatu, Marshall Islands and Hawaii) in the Pacific. We examine TCs across 20 models from the Coupled Model Intercomparison Project phase 5 database12, forced under historical and greenhouse warming conditions. The 12 most realistic models identified show a strong consensus on El Niño-driven changes in future-climate large-scale environmental conditions that modulate development of TCs over the off-equatorial western Pacific and the central North Pacific regions. These results have important implications for climate change and adaptation pathways for the vulnerable Pacific island nations.