Depth profiles of sediment thermal conductivity are required for understanding the thermal structure in active seismogenic zones. During the Nankai Trough Seismogenic Zone Experiment (NanTroSEIZE), a scientific drilling project of the International Ocean Discovery Program, a borehole penetrated to a depth of 3262.5 meters below seafloor (mbsf) at site C0002. Because core samples obtained from below ~1100 mbsf in an accretionary prism are limited, a thermal conductivity profile over such depths usually determined by laboratory measurements using core samples is not available. To obtain the thermal conductivity profile at site C0002, we used core samples collected from sediments that overlay the in-coming subducting oceanic basement at NanTroSEIZE site C0012, which can be considered to have the same mineral composition as the accretional prism at site C0002. The thermal conductivity of the C0012 core samples was measured at high pressure to simulate subduction by reducing the sample porosity. We measured the thermal conductivity of six core samples from 144–518 mbsf at site C0012 up to a maximum effective pressure of ~50 MPa, corresponding to depths greater than ~4 kmbsf. We obtained an empirical relation between thermal conductivity and fractional porosity for the Nankai Trough accretionary prism as = exp(-1.09φ+0.977). Based on porosity data measured using core/cuttings samples and data derived from P-wave velocity logs, we estimate two consistent and complete thermal conductivity profiles down to ~3 kmbsf in the Nankai Trough accretionary prism. These profiles are consistent with the existing thermal conductivity data measured using limited core samples.