The equatorial cold tongue (ECT) of the eastern Pacific is the most dynamic ocean region in the world's tropics and sets the tempo for global climate anomalies arising from El Niño–Southern Oscillation (ENSO) events. This region's deglaciation history and relationship with north and south polar climates remains poorly understood, impeding integration of tropical Pacific ocean-atmosphere dynamics and ENSO variability in our understanding of glacial cycles. Here we present alkenone reconstructions of sea surface temperature (SST) across the last glacial termination from five ECT cores east of the Galapagos Islands. A composite index of SST based on these demonstrates strong temporal affinity with the two-step deglaciation of the Northern Hemisphere, composed of two distinct warming steps at the beginning of the Bölling and the end of the Younger Dryas intervals. Within dating uncertainty, warming in the ECT began in phase with the Bölling excursion, was followed by a 2–3 ka plateau, and resumed with a second pulse at the end of the Younger Dryas. On the basis of our reconstructions, about two thirds of the warming materialized at or after the end of the Younger Dryas, implying a marked delay in the region's response to deglaciation. The results challenge the prevailing paradigm that ECT deglacial history conforms to an Antarctic timing, commonly attributed to advection from the Southern Ocean through an interior oceanic link, or to synchronous response of both regions to CO2 forcing. Our results emphasize instead the role of dynamical adjustments linked to Northern Hemisphere processes, most likely transmitted through the atmosphere.