The aim of this study was to investigate the effects of a rehabilitation exercise for people with incomplete Spinal Cord Injury (iSCI), based on cycling and combined afferent electrical stimulation (ES-cycling), to normalize spinal activity in response to a plantar cutaneous stimulation. We studied Soleus H-reflex excitability following ipsilateral plantar electrical stimulation applied at 25–100 ms inter-stimulus intervals (ISI’s), on 13 non-injured subjects and 10 subjects with iSCI. Reflexes were tested before and after a 10 min session of ES-cycling to evaluate the effects of the exercise. Plantar-conditioned H-reflex modulation increased in the iSCI group after ES-cycling, compared to the limited modulation observed before the exercise. Conversely, the non-injured group presented pronounced modulation both before and after the exercise. We conclude that ES-cycling improved plantar-conditioned spinal neuronal excitability in subjects with iSCI. Results could be used in the design of more effective leg-cycling therapies, to promote central neuroplasticity and rehabilitation in lower limb muscle activity following iSCI.