Silica precipitation is assumed to play a significant role in post-earthquake recovery of the mechanical and hydrological properties of seismogenic zones. However, the relationship between the widespread quartz veins around seismogenic zones and earthquake recurrence is poorly understood. Here we propose a novel model of quartz vein formation associated with fluid advection from host rocks and silica precipitation in a crack, in order to quantify the timescale of crack sealing. When applied to sets of extensional quartz veins around the Nobeoka Thrust of SW Japan, an ancient seismogenic splay fault, our model indicates that a fluid pressure drop of 10-25 MPa facilitates the formation of typical extensional quartz veins over a period of 6.6 × 100-5.6 × 101 years, and that 89%-100% of porosity is recovered within ~3 × 102 years. The former and latter sealing timescales correspond to the extensional stress period (~3 × 101 years) and the recurrence interval of megaearthquakes in the Nankai Trough (~3 × 102 years), respectively. We therefore suggest that silica precipitation in the accretionary wedge controls the recurrence interval of large earthquakes in subduction zones.