In this paper, we describe the effects of vacuum annealing on the mechanical properties of gallium (Ga)-implanted silicon (Si) nanowires (NWs) obtained by focused ion beam (FIB) fabrication. We have particularly developed a micro-electromechanical system (MEMS)-based tensile test device to enable us to directly apply tension to nanoscale Si NWs. The nonannealed and annealed Si NWs made from a silicon-on-nothing (SON) membrane were prepared. The Ga-implanted Si NWs, which were sampled on the MEMS device without FIB irradiation, were annealed at 700 °C for 10 s to 60 min in high vacuum. The quasi-static uniaxial tensile tests of all the NWs were conducted by in situ scanning electron microscopy (SEM). The dependences of annealing time on Young’s modulus and fracture strength were observed. Young’s modulus gradually recovered with increasing annealing time, whereas the strength dropped first at 10 s of annealing and then slightly increased with annealing time. The difference in the recovery process between these characteristics was discussed from the viewpoint of crystallinity-damage recovery.