Abstract Climate model simulations of El Niño–Southern Oscillation (ENSO) behavior for the last millennium demonstrate interdecadal to centennial changes in ENSO variability that can arise purely from stochastic processes internal to the climate system. That said, the instrumental record of ENSO does not have the temporal coverage needed to capture the full range of natural ENSO variability observed in long, unforced climate model simulations. Here we demonstrate a probabilistic framework to quantify changes in ENSO variability via histograms and probability density functions using monthly instrumental and coral‐based sea surface temperature (SST) anomalies from 1900–2005 and 1051–1150 CE. We find that reconstructed SST anomalies from modern corals from the southwest Pacific capture changes in ENSO variability that are consistent with instrumental SST data from the central equatorial Pacific. Fossil coral records indicate 100 years of relatively lower ENSO variability during part of the Medieval Climate Anomaly. Our results demonstrate that periods of reduced ENSO variability can last a century, far longer in duration than modern observations in the instrumental record of ENSO, but consistent with results from unforced climate model simulations.