Athletes in collision sports frequently sustain repetitive head impacts (RHI), which, while not individually severe enough for a clinical mild traumatic brain injury (mTBI) diagnosis, can compromise neuronal organization by transferring mechanical energy to the brain. Although numerous studies target athletes with mTBI, there is a lack of longitudinal research on young collision sport participants, highlighting an unaddressed concern regarding cumulative RHI effects on brain microstructures. Therefore, this study aimed to investigate the microstructural changes in the brains' of high school rugby players due to repeated head impacts and to establish a correlation between clinical symptoms, cumulative effects of RHI exposure, and changes in the brain's microstructure. We conducted a longitudinal magnetic resonance imaging (MRI) study on 36 male high school rugby players across a season using 3D T1-weighted and multi-shell diffusion MRI sequences, comparing them with 20 matched controls. Players with concussions were separately tracked up to 6 weeks post-injury with three-times scans within this period. The Sport Concussion Assessment Tool (SCAT5) symptom scale assessed mTBI symptoms, and mouthguard-embedded kinematic sensors recorded head impacts. No significant volumetric changes in subcortical structures were found post-rugby season. However, there were substantial differences in mean diffusivity (MD) and axial diffusivity (AD) between the rugby players and controls across widespread brain regions. Diffusion metrics, especially AD, MD, and radial diffusivity of certain brain tracts, displayed strong correlations with SCAT5 symptom severity. Repeated head impacts during a rugby season may adversely affect the structural organization of the brain's white matter. The observed diffusion changes, closely tied to SCAT5 symptom burden, stress the profound effects of seasonal head impacts and highlight individual variability in response to repetitive head impact exposure. To better manage sports-related mTBI and guide return-to-play decisions, comprehensive studies on brain injury mechanisms and recovery post-mTBI/RHI exposure are required.