Neuronal and vascular reorganization after spinal cord injury (SCI) is scarcely known although its characterization has major implications in understanding the functioning of the altered spinal cord. Several electrophysiological and anatomical lines of evidence support plasticity caudal to the lesion site, but do not provide sufficient clues about neuronal and vascular reorganization after SCI. The aim of the present study was to compare neuronal activation in the lumbar spinal cord between uninjured and SCI rats with novel optical imaging technology. The results showed significant haemodynamic response differences after sciatic nerve stimulation in uninjured controls, in comparison to SCI rats. Both timing and shape of the response were modified. In uninjured rats, blood flow presented an initial dip but was rapidly drained from the activation site through the venous system. In comparison, the blood transfer rate in SCI rats was much slower. Damaged blood vessels at the lesion site after thoracic SCI impacted the vascular response upon neuronal activation in the lumbar spinal cord. This observation is important in the study of spinal cord function after SCI by imaging techniques based on haemodynamics (blood oxygenation level-dependent using functional magnetic resonance imaging (BOLD fMRI) and optical imaging). In conclusion, our results indicate that new avenues quantifying the influence of vascular plumbing will have to be developed to explore the efficacy of rehabilitation and pharmacological therapies by haemodynamic imaging.