There is growing evidence that peripheral motor axons deteriorate following spinal cord injury (SCI). Secondary axonal dysfunction can exacerbate muscle atrophy and contribute to peripheral neuropathies and neuropathic pain and lead to further functional impairment. In an attempt to ameliorate the adverse downstream effects that developed after SCI, the effects of a short-term peripheral nerve stimulation (PNS) program on motor axonal excitability in 22 SCI patients was investigated. Axonal excitability studies were undertaken in the median and common peroneal nerves (CPN) bilaterally prior to and following a 6-week unilateral PNS program. PNS was delivered percutaneously over the median nerve at the wrist and CPN around the fibular head and the compound muscle action potential (CMAP) from the abductor pollicis brevis and tibialis anterior recorded. Stimulus intensity was above motor threshold and pulses (450 µsec) were delivered at 100 Hz with a 2 second on/off cycle for 30 minutes, 5 days per week. SCI patients had consistently high thresholds with a reduced CMAP consistent with axonal loss; in some patients the peripheral nerves were completely inexcitable. Nerve excitability studies showed profound changes in membrane potential, with a “fanned-in” appearance in threshold electrotonus, consistent with membrane depolarisation, and significantly reduced superexcitability during the recovery cycle. These membrane dysfunctions were ameliorated after 6 weeks of PNS, which produced a significant hyperpolarising effect. The contralateral, non-stimulated nerves remained depolarised. Short-term PNS reversed axonal dysfunction following SCI and could offer an opportunity to prevent chronic changes in axonal and muscular function and may improve rehabilitation outcomes.