Changes in El Niño–Southern Oscillation (ENSO) variability are difficult to extract from paleoceanographic reconstructions because they are superimposed on changes in seasonal variability that modulate the first-order climate signal. Here we address this problem by reconstructing thermocline structure from a marine sediment core retrieved from the eastern equatorial Pacific. At the core location, changes in hydrologic parameters within the thermocline are linked to ENSO activity, with a reduced influence of seasonal variability compared to surface waters. We performed repeated isotopic analyses (δ18O) on single specimens of the thermocline-dwelling planktonic foraminifera Neogloboquadrina dutertrei at several targeted time periods over the last 50 ka to extract the total thermocline variance, a parameter supposed to reveal changes in ENSO. No fundamental changes in amplitude and frequency of the events were detected despite differences in climatic background. However, our data suggest that long-term variations in the thermocline variability occurred over the last 50 ka, with the highest and lowest ENSO activities occurring during the last glacial period and the Last Glacial Maximum, respectively.