Abstract Changes in cloud fraction associated with Central Pacific and Eastern Pacific El Niños are analyzed using monthly cloud data from the International Satellite Cloud Climatology Project, meteorological variables from the European Center for Medium Range Weather Forecasting reanalysis version 5, and radiation data from the Clouds and the Earth’s Radiant Energy System. We observe robust increases in low cloud fraction in the tropical Southeast Pacific (SEP, 120°–80°W 0°–20°S) during El Niños. The increases in SEP low‐cloudiness are associated with CP‐El Niño variability. Increases in SEP Sea Surface Temperature during CP‐El Niños are accompanied by a warmer tropical free troposphere, increased cold advection, and reduced overlying cirrus, facilitating the growth of low clouds. Northeast Pacific cloud decks decrease during El Niños, consistent with weaker free‐tropospheric heating outside the tropics. Coupled CMIP6 model experiments are unable to replicate increased SEP low cloud due to a misrepresentation of El Niño Southern Oscillation diversity.