The purpose of this study was to investigate the efficacy of bypass nerve grafting with end-to-side neurorrhaphy in repair of the partial nerve injury in a rabbit model. Thirty-six adult male New Zealand rabbits were divided into three groups. A partial nerve injury was created by removal of a segment of the lateral fascicle of the left peroneal nerve. In group one, the injured nerve was repaired with nerve graft bypassing the injury site in an end-to-side fashion 4 weeks after injury. In group two, the injured nerve was repaired with end-to-end interpositional nerve grafting 6 weeks after injury. The injured nerve without repair was used as the control. Sixteen weeks after nerve repair, in groups one and two, and 20 weeks after the initial nerve injury in the control group, the nerves were dissected for electrophysiological examination and biopsied for histology and molecular markers expression. The nerve repair with interpositional nerve grafting achieved maximal functional recovery. However, motor nerve conduction velocity and compound motor action potential in nerve repair with bypass nerve grafting were significantly higher than that in the nerve injury without repair. Histologically, the regenerated myelinated axons and unmyelinated axons were present in the distal peroneal nerves in the bypass nerve grafts. The axon counts in nerve repair with the bypass nerve grafting were also significantly higher than that in the nerve injury without repair. The comparisons of the ciliary neurotrophic factor and the calcitonin gene-related peptide gene expressions between nerves with and without repair were significantly different. End-to-side bypass nerve grafting can significantly improve functional recovery in the nerve with partial injury and may be a useful repair strategy in neuromas-in-continuity.