Accumulating clinical evidence suggests remote neurodegeneration occurs in non-ischemic brain regions distant to the site of infarction in stroke, driven by both axonal degeneration and global brain inflammation. Prior preclinical studies of remote degeneration have mainly focused on brain changes over a few days or weeks post-stroke. We investigated long-term structural brain changes in an endothelin-1 model of mild focal ischemic stroke in rats, using a clinically relevant period of 48-weeks. Serial structural and diffusion-weighted MRI data were used to assess dynamic volume and white matter trajectories. We found significant cortical atrophy and white matter alterations, suggesting widespread stroke-related degenerations.