The appearance of permanent El Niño–like conditions prior to 3 million years ago is founded on sea-surface temperature (SST) reconstructions that show invariant Pacific warm pool temperatures and negligible equatorial zonal temperature gradients. However, only a few SST records are available, and these are potentially compromised by changes in seawater chemistry, diagenesis, and calibration limitations. For this study, we establish new biomarker-SST records and show that the Pacific warm pool was ~4°C warmer 12 million years ago. Both the warm pool and cold tongue slowly cooled toward modern conditions while maintaining a zonal temperature gradient of ~3°C in the late Miocene, which increased during the Plio-Pleistocene. Our results contrast with previous temperature reconstructions that support the supposition of a permanent El Niño–like state.