Recent reports suggest that rehabilitation measures that increase physical activity of patients can improve functional outcome after incomplete spinal cord injuries (iSCI). To investigate the structural basis of exercise-induced recovery, we examined local and remote consequences of voluntary wheel training in spinal cord injured female mice. In particular, we explored how enhanced voluntary exercise influences the neuronal and glial response at the lesion site as well as the rewiring of supraspinal tracts after iSCI. We chose voluntary exercise initiated by providing mice with free access to running wheels over "forced overuse" paradigms because the latter, at least in some cases, can lead to worsening of functional outcomes after SCI. Our results show that mice extensively use their running wheels not only before but also after injury reaching their pre-lesion exercise levels within five days after injury. Enhanced voluntary exercise improved their overall and skilled motor function after injury. In addition, exercising mice started to recover earlier and reached better sustained performance levels. These improvements in motor performance are accompanied by early changes of axonal and glial response at the lesion site and persistent enhancements of the rewiring of supraspinal connections that resulted in a strengthening of both indirect and direct inputs to lumbar motoneurons.