Microcracks in fault damage zones can heal under thermally controlled processes. If a flow communication exists between a fluid source and the fault damage zone, warm fluids can migrate into it, change its thermal conditions, and assist healing. The crack life span depends on the local temperature and is, thus, modified by the infiltration of warm fluids. The features of the initial fault architecture govern how the fluids will propagate within the fault damage zones. This affects the rate of healing and the rate of permeability reduction. The region infiltrated by fluids will then show a significant decrease in its permeability, as seen in many field examples like the Alpine Fault. Conventionally, the damage zones immediately near the fault core have a high permeability that decays as we go further away. However, the region adjacent to the fault core, in the Alpine Fault, New Zealand, has the lowest permeability in the current interseismic period. As shown by our simulations, this can be due to healing and sealing, favored by the localized high geothermal gradients (confirmed by the drilling data) and the upward fluid migration through the fault relay structure, which accelerated mass diffusion and minerals precipitation.