The transition from the Pliocene to the Pleistocene was accompanied by major tectonic reorganizations of key oceanic gateways. In particular, the gradual closure of the Panama Gateway and the constriction of the Indonesian Gateway significantly affected the structure of the Pacific thermocline. In the East Pacific, the thermocline shoaled from an early Pliocene El Niño‐like depth to its modern state, which had significant implications for global climate. Here we use Mg/Ca temperature estimates from subsurface and thermocline dwelling foraminifera to reconstruct the meridional Plio‐Pleistocene evolution of the Southeast Pacific thermocline, in relation to atmospheric circulation changes. In combination with similar reconstructions from the north‐equatorial Pacific, our data indicate a change in the thermocline, responding to the northward displacement of the Intertropical Convergence Zone/South Pacific High system between ~3.8 and 3.5 Ma. After 3.5 Ma, we record a second major phase of thermocline shoaling, which points to the Intertropical Convergence Zone/South Pacific High‐system movement toward its modern position along with the gradual cooling of the Northern Hemisphere and its associated glaciation. These findings highlight that a warming globe may affect equatorial regions more intensively due to the potential temperature‐driven movement of the Intertropical Convergence Zone/South Pacific High and their associated oceanic systems.