Background: There is presently no cure for locomotor deficits after spinal cord injury (SCI). Very few therapies effectively target the brain due to poor understanding of the brain’s role post-SCI. Newly developed tissue clearing techniques have permitted unbiased three-dimensional circuit analysis, opening new opportunities for SCI-related brain interrogation. Methods: We established a novel brain interrogation pipeline by optimizing mouse brain clearing, imaging, and atlas registration. We leveraged a spontaneous recovery lateral hemisection model to analyze whole brain cell activity and connectivity with the lumbar cord using cFos immunolabelling and virus-mediated projection tracing. We identified a functionally and anatomically dynamic region correlating with recovery and interrogated its locomotor role with optogenetics. We assessed deep brain electrical stimulation (DBS) of this region in a more clinically relevant rat contusion SCI using an established bipedal robotic interface. Results: We unexpectedly uncovered the lateral hypothalamus (LH) to functionally and anatomically correlate with recovery. LHVglut2 optogenetic stimulation significantly augmented locomotor function. LH DBS in rats acutely robustly augmented bipedal locomotion post-SCI. Conclusions: This is the first demonstration of the LH’s role in locomotion post-SCI and is a novel DBS target that robustly augmented locomotor function, dependent on LH glutamatergic cells. LH DBS may be a promising intervention in humans.