Spinal cord injury (SCI) induces secondary damage characterized by mitochondrial dysfunction, oxidative stress, and apoptosis, which collectively impede neurological recovery. Elamipretide (SS-31) is a mitochondria-targeting peptide with potential neuroprotective effects. Here, we investigated whether SS-31 improves functional outcomes after contusive SCI and explored associated mechanisms. In a mouse thoracic contusion model, SS-31 treatment significantly enhanced locomotor recovery and gait performance. Histological analyses showed reduced lesion pathology and increased neuronal preservation in the injured spinal cord. Early after injury, SS-31 attenuated apoptosis signaling, evidenced by reduced cleaved caspase-3 and Bax and increased Bcl-2. At the chronic stage, SS-31 was associated with diminished astrogliosis and enhanced markers of axonal and synaptic remodeling. In oxidatively stressed PC12 cells, SS-31 preserved mitochondrial membrane potential, reduced ROS accumulation, and supported oxidative phosphorylation-related protein integrity. Collectively, these findings suggest that SS-31 promotes recovery after SCI, potentially by mitigating early apoptotic injury and supporting mitochondrial homeostasis and neural remodeling.