Transform faults accommodate the lateral motions between lithospheric plates, producing large earthquakes. Away from active transform boundaries, former oceanic transform faults also form the fracture zones that cover the ocean floor. However, the deep structure of these faults remains enigmatic. Here we present ultra-long offset seismic data from the Romanche transform fault in the equatorial Atlantic Ocean that indicates the presence of a low-velocity anomaly extending to similar to 60 km below sea level. We performed three-dimensional thermal modelling that suggests the anomaly is probably due to extensive serpentinization down to similar to 16 km, overlying a hydrated, shear mylonite zone down to 32 km. The water is considered to be sourced from seawater-derived fluids that infiltrate deep into the fault. Below 32 km is interpreted to be a low-temperature, water-induced melting zone that elevates the lithosphere-asthenosphere boundary, causing substantial thinning of the lithosphere at the transform fault. The presence of a thinned lithosphere at transform faults could explain observations of volcanism, thickened crust and intra-transform spreading centres at transform faults. It also suggests that migration and mixing of water-induced melt with the high-temperature melt may occur beneath the ridge axis.