Ion implantation is widely used to fabricate advanced optical and optoelectronic materials and devices. However, nanoscale defects generated during the ion implantation process severely affect the quality and properties of the material and device. Here, combining computational simulations and experiments, we investigate the mechanism for defect repair in fused silica after Cu ion implantation using femtosecond laser irradiation with an energy fluence much lower than the ablation threshold. Atomic force microscopy demonstrates no unexpected ablation. The optical absorption spectra show that various types of defects with formation energies between 1.9 and 6.2 eV can be repaired successfully via an athermal procedure. The Raman spectra imply that the broken chemical bonds reconnect after femtosecond laser irradiation. Our study reveals that low-energy femtosecond laser irradiation can transfer the appropriate energy needed to repair defects; thus it could be useful in fabricating nonlinear optical devices due to its high spatial selectivity and convenience.