The Southern Ocean is a primary heat sink that buffers atmospheric warming and has warmed substantially, accounting for an outsized portion of global warming-induced excess heat in the climate system. However, its projected warming is highly uncertain and varies substantially across climate models. Here, using outputs from Coupled Model Intercomparison Project phase six models, we show that Southern Ocean warming during the twenty-first century is linked to the change in amplitude of the El Niño–Southern Oscillation (ENSO). Models simulating a larger increase in ENSO amplitude systematically produce a slower Southern Ocean warming; conversely, a smaller increase in ENSO amplitude sees a stronger warming. The asymmetry in amplitude and teleconnection between El Niño and La Niña produce cumulative surface wind anomalies over the southern high latitudes, impacting Southern Ocean heat uptake. The magnitude of inter-model ENSO variations accounts for about 50% of the uncertainty in the projected Southern Ocean warming.