The early Paleogene represents the most recent interval in Earth's history characterized by global greenhouse warmth on multi-million year timescales, yet our understanding of long-term climate and carbon cycle evolution in the low latitudes, and in particular the Indian Ocean, remains very poorly constrained. Here we present the first long-term sub-eccentricity-resolution stable isotope ( and ) and trace element (Mg/Ca and B/Ca) records spanning the late Paleocene–early Eocene (∼58–53 Ma) across a surface–deep hydrographic reconstruction of the northern Indian Ocean, resolving late Paleocene 405-kyr paced cyclicity and a portion of the PETM recovery. Our new records reveal a long-term warming of ∼4–5 °C at all depths in the water column, with absolute surface ocean temperatures and magnitudes of warming comparable to the low latitude Pacific. As a result of warming, we observe a long-term increase in of the mixed layer, implying an increase in net evaporation. We also observe a collapse in the temperature gradient between mixed layer- and thermocline-dwelling species from ∼57–54 Ma, potentially due to either the development of a more homogeneous water column with a thicker mixed layer, or depth migration of the Morozovella in response to warming. Synchronous warming at both low and high latitudes, along with decreasing B/Ca ratios in planktic foraminifera indicating a decrease in ocean pH and/or increasing dissolved inorganic carbon, suggest that global climate was forced by rising atmospheric CO2 concentrations during this time.