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.Plain Language Summary Over the course of the last 5 million years (Ma), two oceanic gateways experienced changes due to major tectonic reorganizations. At~4.4 Ma, the passage connecting the Atlantic and Pacific closed when the connection between the Americasthe Panama land bridgeformed. On the western side of the Pacific, the formation of volcanic islands around Indonesia and Papua New Guinea at~3.5-3 Ma hampered the transport of tropical water from the Pacific into the Indian Ocean. These processes significantly changed the ocean dynamics and should have altered the tropical Pacific temperature distribution from potential permanent El Niño-like conditions (warm west, warm east) to the modern state. We present sea surface and subsurface temperature reconstructions for the tropical East Pacific off Chile covering the last 5 Ma. Our data imply that the Intertropical Convergence Zone and the South Pacific High moved toward the north along with the warming Northern Hemisphere from~3.8 to 3.5 Ma. Parallel to the subsequent cooling and glaciation of the Northern Hemisphere, the East Pacific Intertropical Convergence Zone/South Pacific High gradually moved toward their modern position. Ultimately, our data show how hemispherical warming/cooling can affect the position of the Intertropical Convergence Zone/South Pacific High and their associated systems of oceanic temperatures.