Vigorous fluid circulation maintained in newly subducted ocean crust significantly affects subduction zone temperatures on the Nankai margin, Japan. The shallow part of the igneous ocean crust is pervasively fractured and thus highly permeable, allowing vigorous hydro thermal circulation. This circulation has been recognized as an important control on the thermal budget and evolution of ocean crust worldwide. However, existing subduction zone thermal models either do not include hydrothermal circulation in ocean crust or assume that it abruptly stops upon subduction. Here we use a conductive proxy to incorporate the thermal effects of high Nusselt number fluid circulation in subducting crust into a subduction zone thermal model. Hydrothermal circulation reduces temperatures in the seismogenic zone of the Nankai margin plate boundary fault by ~20 °C at the updip limit of seismicity and ~100 °C at the downdip limit. With improved thermal models for subduction zones that include the effects of hydrothermal circulation in subducting crust, estimates of metamorphic reaction progress and interpretations of fault zone processes on various margins may need to be revisited.