Traumatic brain injury (TBI) is associated with gray and white matter alterations in brain tissue. Gray matter alterations are not yet as well studied as those of the white matter counterpart. This work utilized T2-weighted structural imaging, diffusion tensor imaging (DTI), and diffusion kurtosis imaging to unveil the gray matter changes induced in a controlled cortical impact (CCI) mouse model of TBI at 5 h, 1 day, 3 days, 7 days, 14 days, and 30 days post-CCI. A cross-sectional histopathology approach was used to confer validity of the magnetic resonance imaging (MRI) data by performing cresyl violet staining and glial fibrillary acidic protein (GFAP) immunohistochemistry. The results demonstrated a significant increase in lesion volume up to 3 days post-injury followed by a significant decrease in the cavity volume for the period of 1 month. GFAP signals peaked on Day 7 and persisted until Day 30 in both ipsilateral and contralateral hippocampus, ipsilateral cortex, and thalamic areas. An increase in fractional anisotropy (FA) was seen at Day 7 in the pericontusional area but decreased FA in the contralateral cortex, hippocampus, and thalamus. Mean diffusivity (MD) was significantly lower in the pericontusional cortex. Increased MD and decreased mean kurtosis were limited to the injury site on Days 7 to 30 and to the contralateral hippocampus and thalamus on Days 3 and 7. This work is one of the few cross-sectional studies to demonstrate a link between MRI measures and histopathological readings to track gray matter changes in the progression of TBI.