Deep-time palaeoclimate studies are vitally important for developing a complete understanding of climate responses to changes in the atmospheric carbon dioxide concentration (that is, the atmospheric partial pressure of CO2, p(CO2))(1). Although past studies have explored these responses during portions of the Cenozoic era (the most recent 65.5 million years (Myr) of Earth history), comparatively little is known about the climate of the late Miocene (similar to 12-5 Myr ago), an interval with p(CO2) values of only 200-350 parts per million by volume but nearly ice-free conditions in the Northern Hemisphere(2,3) and warmer-than-modern temperatures on the continents(4). Here we present quantitative geochemical sea surface temperature estimates from the Miocene mid-latitude North Pacific Ocean, and show that oceanic warmth persisted throughout the interval of low p(CO2) similar to 12-5 Myr ago. We also present new stable isotope measurements from the western equatorial Pacific that, in conjunction with previously published data(5-10), reveal a long-term trend of thermocline shoaling in the equatorial Pacific since similar to 13 Myr ago. We propose that a relatively deep global thermocline, reductions in low-latitude gradients in sea surface temperature, and cloud and water vapour feedbacks may help to explain the warmth of the late Miocene. Additional shoaling of the thermocline after 5 Myr ago probably explains the stronger coupling between p(CO2), sea surface temperatures and climate that is characteristic of the more recent Pliocene and Pleistocene epochs(11,12).