The role of plate tectonics in the deep carbon cycle is crucial for understanding Earth’s climate, planetary life, and atmospheric CO2 over geological time; however, knowledge of carbon sources and sinks is dependent on reconstructed plate tectonic histories. Intra-oceanic subduction (i.e. subduction of an oceanic plate beneath another oceanic plate) is a recognized knowledge gap in plate tectonic reconstructions, especially within Pacific-Panthalassa, because continuous recycling of oceanic plates into the mantle leaves fewer geological traces. We examine the role of unassessed intra-oceanic subduction on paleoclimate reconstructions since the Mesozoic. We compare two global plate reconstructions: ”Tomopac” version 1, which integrates tomography and other constraints to enhance intra-oceanic subduction histories within Pacific-Panthalassa; and a widely-used model that implements less intra-oceanic subduction (Matthews et al., 2016). We model global seafloor ages, estimate total and areal subducted carbon since 200 Ma, and input subduction histories into the COPSE biogeochemical model (Lenton et al., 2021) to compare predicted global atmospheric CO2 and mean surface temperature histories. Tomopac with more intra-oceanic subduction shows a ~5% increase in global subduction zone lengths but a ~8% decrease in global subducted area and slab flux since 200 Myr. Overall, contrasted intra-oceanic subduction histories since 200 Ma alter estimates of subducted carbon by ~15-20%. Incorporating previously unassessed intra-oceanic subduction from Tomopac in COPSE reduces global mean surface temperatures up to 2°C and reduces atmospheric CO2 up to 300 ppm from 200 Ma to present, highlighting the importance of recognizing intra-oceanic subduction in modulating Earth’s long-term paleoclimate.