Projected Antarctic shelf ocean warming controls the pace of Antarctic ice sheet melt but varies vastly across climate models. A projected increase in El Niño variability is found to slow future midlatitude Southern Ocean warming but its impact on Antarctic shelf ocean is unknow.  Here we show that, opposite to slowing the midlatitude Southern Ocean warming, a projected increase in El Niño-Southern Oscillation variability accelerates future Antarctic shelf ocean warming. The inter-model variations in ENSO response account for ~40% of the uncertainty in the projected warming.