Reconstructions of Pliocene sea-surface temperature (SST) gradients and thermocline depths suggest that the zonal temperature gradient of the tropical Pacific was distinct from the modern. However, the nature of any El Niño–Southern Oscillation (ENSO) variability superimposed on this mean state is difficult to determine. We developed monthly resolved multidecadal stable isotopic time series from an extremely well preserved central Caribbean coral dating to the Miocene-Pliocene transition, prior to closure of the Central American Seaway (CAS). Paleoceanographic modeling suggests that the flow of water associated with El Niño and La Niña events through the CAS allowed Caribbean corals to record the ENSO-related SST anomalies. Spectral analysis of coral oxygen isotope ratios reveals periodicities similar to modern ENSO signatures, suggesting that ENSO-like variability characterized the Miocene-Pliocene transition.