Neuroimaging studies suggest that spinal cord injury (SCI) may lead to significant anatomical alterations in the human sensorimotor system. In particular, voxel-based morphometry (VBM) of cortical volume has revealed a significant gray and white matter atrophy bilaterally in the primary sensory cortex (S1). By contrast, some structural studies failed to detect changes in gray matter volume (GMV) in the primary motor cortex (M1) following SCI, whereas others have reported a substantial decrease of GMV also in M1. In addition to direct degeneration of the sensorimotor cortex, SCI can also lead to atrophy of the non-sensorimotor cortex, such as anterior cingulate cortex, insular cortex, middle frontal gyrus and supplementary motor area. These findings suggest that SCI can cause remote atrophy of brain gray matter in the salient network. Furthermore, pain-related remodelling may occur in SCI. In fact, structural changes in SCI are also related to the presence and degree of below-level pain. We performed a systematic review of the neuroimaging studies showing morphometric cortical changes and subsequent functional reorganization in humans with SCI. Literature search was conducted using PubMed and Embase. We identified 12 articles matching the inclusion criteria and 195 patients were included in these studies. The wide range of disease duration, rehabilitation training, drug intervention, and different research methodology, especially the identification of region of interest and the statistical approach to correct for multiple comparisons, may have contributed to some inconsistencies between the reviewed studies. Nevertheless, neuroimaging biomarkers can assess the extent of neural damage, elucidate the mechanisms of neural repair, and predict clinical outcome. A better understanding of the structural and functional changes that occur at cortical level following SCI may be useful in tracking potential treatment induced changes and identifying potential therapeutic targets, thus developing evidence-based rehabilitation therapies.