Preserved or restored integrity of the corticospinal tract (CST) is critical for motor recovery after stroke. However, data on spatiotemporal alterations in CST integrity after stroke are largely lacking. Here we implemented diffusion tensor-based tractography to identify the CST in rat brain, which we applied to measure microstructural changes along the CST following experimental stroke to the sensorimotor cortex. Number of tractography streamlines, fractional anisotropy (FA) and axial diffusivity (AD) were reduced 1 week post-stroke, and recovered to control levels after 28 weeks. This temporal pattern, reflective of white matter remodeling, coincided with loss and recovery of sensorimotor function.