Spinal cord injury (SCI) leads to severe motor and sensory deficits. New advances in non-invasive neuromodulation technologies such as transcranial magnetic stimulation (TMS) have shown promise in facilitating recovery following brain injuries. Here we tested whether TMS therapy can be developed as a rehabilitative approach in a rat model of SCI. High-resolution functional MRI (fMRI) at 11.7 T was used to detect cortical activity associated with post-injury neuroplasticity. A battery of behavioral tests was used to monitor gross changes in motor behavior. Our results demonstrate that TMS therapy is beneficial in improving post-SCI functional outcomes.