We report detailed thermal measurements undertaken during Integrated Ocean Drilling Program (IODP) Expeditions 315 and 316 along the Nankai Trough Seismogenic Zone Experiment (NanTroSEIZE) transect offshore the Kii Peninsula, Japan. Geothermal objectives included determining thermophysical rock properties of the cored material and characterizing the background thermal regime along this transect. New thermal conductivity measurements made with a divided bar are reported and supplement shipboard full- and half-space thermal conductivity measurements for a total of 938 thermal conductivity measurements. Thermal conductivity varies between about 1.0 W m−1 K−1 near the seafloor to 1.6 W m−1 K−1 at a depth of 1 km. Thermal conductivity generally increases with depth and correlates with variations in porosity and lithology. Thermal gradients along the transect are characterized by 48 sediment temperature measurements from 6 sites. Thermal corrections for the effects of bathymetric relief and sedimentation improve the confidence with which the heat flow values can be interpreted. Heat flow generally decreases with landward distance from the deformation front and varies from 70 mW m−2 just landward of the deformation front to 54 mW m−2 at sites characterizing the outer fore-arc high and to 57 mW m−2 at the Kumano Basin Site. IODP heat flow measurements are significantly lower than nearby seafloor heat flow measurements. This difference is most likely due to variations in bottom water temperature that have a large effect on values of seafloor heat flow. Thus the heat flow of the Nankai accretionary prism is lower than previously thought. We present thermal models of subduction along this transect and explore the impact of the initial geotherm. Conductive plate cooling based on the age of subducting seafloor (20 Myr) under predicts the observed heat flow. We find a good fit to the data using a geotherm appropriate for 10 Myr seafloor. The extra heat is interpreted in terms of back-arc thermal environments.