Background: Functional electrical stimulation (FES) has been found to be effective in restoring voluntary functions after spinal cord injury (SCI) and stroke. However, the central nervous system (CNS) changes that occur in as a result of this therapy are largely unknown. Objective: To examine the effects of FES on the restoration of voluntary locomotor function of the CNS in a SCI rat model. Methods: SCI rats were instrumented with chronic FES electrodes in the hindlimb muscles and were divided into two groups: (a) FES therapy and (b) sedentary. At day 7 post-SCI, the animals were assessed for locomotion performance by using a Basso, Beattie and Bresnahan (BBB) scale. They were then anesthetized for a terminal in vivo experiment. The lumbar spinal cord and somatosensory cortex were exposed and the instrumented muscles were stimulated electrically. Associated neurovascular responses in the CNS were recorded with an intrinsic optical imaging system. Results: FES greatly improved locomotion recovery by day 7 post-SCI, as measured by BBB scores (P < 0.05): (a) FES 10 ± 2 and (b) controls 3 ± 1. Furthermore, the FES group showed a significant increase (P < 0.05) of neurovascular activation in the spinal cord and somatosensory cortex when the muscles were stimulated between 1 and 3 motor threshold (MT). Conclusion: Hind limb rehabilitation with FES is an effective strategy to improve locomotion during the acute phase post-SCI. The results of this study indicate that after FES, the CNS preserves/acquires the capacity to respond to peripheral electrical stimulation.