End-to-side (ETS) neurorrhaphy has been applied in the repair of peripheral nerve injuries and in babysitter procedures. However, the long-term changes of donor nerve and muscle after ETS remain unknown. This study was designed to investigate long-term changes in donor nerve and muscle in a rat model. Sixty Lewis rats were equally allocated into three groups of 20 rats. The peroneal nerve was divided. In Group A, end-to-end (ETE) neurorrhaphy was performed. In Group B, ETS was performed to an epineurial window on the tibial nerve. In Group C, ETS was performed to the tibial nerve with 40% partial neurectomy. The following data were obtained at 6, 12, 18, and 24 weeks postoperatively: latency delaying rate (LDR), amplitude recovery rate (ARR), myelinated fiber counts, muscle force and weight, and cross-sectional area of gastrocnemius muscle fibers. The results showed no significant changes of the donor nerve and muscle in Group B. Nerve regeneration was found in the peroneal nerve, and myelinated fiber number was significantly decreased when compared to the nerve with ETE. In Group C, the myelinated axon number in the peroneal nerve was equivalent to the level in ETE repair. However, function and structure of the donor nerve and muscle were significantly impaired in the early postoperative period. Nonetheless, full recovery was observed 24 weeks after surgery. Both ETS with epineurial window and 40% donor nerve neurectomy showed reinnervation of the recipient nerve without structural and functional changes of the donor system in a long-term follow-up. Partial neurectomy may promote recipient nerve regeneration, but at the cost of donor neuromuscular compromises in the early postoperative period. This study provides long-term evidence for further investigation of ETS in peripheral nerve repair and in babysitter procedures.