Spinal cord injury (SCI) can cause loss of mobility in the limbs, and no drugs, surgical procedures, or rehabilitation strategies provide a complete cure. Exercise capacity is thought to be associated with the causes of many diseases. However, no studies to date have assessed whether congenital exercise ability is related to the recovery of spinal cord injury. High congenital exercise ability (HE) and low congenital exercise ability (LE) mice were artificially bred from the same founder ICR mice. The HE and LE groups still exhibited differences in exercise ability after 13 generations of breeding. Histological staining and immunohistochemistry staining indicated no significant differences between the HE and LE groups on recovery of the spinal cord. In contrast, after SCI, the HE group exhibited better mobility in gait analysis and longer endurance times in the exhaustive swimming test than the LE group. In addition, after SCI, the HE group also exhibited less atrophy than the LE group, and no inflammatory cells appeared. In conclusion, we found that high congenital exercise ability may reduce the rate of muscle atrophy. This result can be applied to sports science and rehabilitation science as a reference for preventive medicine research.