Abstract The interannual El Niño‐Southern Oscillation (ENSO) triggers extreme climate events worldwide. Geochemical proxies in coral skeletons from the eastern equatorial Pacific (EP) track ENSO conditions, constraining its long‐term variance and response to forcing. Multiproxy analysis of three subfossil colonies from the EP Galápagos Islands finds ENSO variability ∼4,000 years before present (BP) was similar to that from 1959 to 1979 CE. These mid‐Holocene results exhibit stronger ENSO variability than that over the preindustrial last millennium, but weaker than that between 1986 and 2016 CE. Whereas positively skewed instrumental and reconstructed temperatures reveal the predominance of warm ENSO events in the modern EP, the corals from 4,000 BP record negatively skewed variance reflecting stronger cold events. The Galápagos results contrast with central equatorial Pacific (CP) coral records identifying minimal ENSO variance from 5,000 to 3,000 BP. Stronger cold events in the EP likely limited CP ENSO variability, creating spatially diverse ENSO signals at 4,000 BP.