There has been growing concern over sports-related brain injuries and their long-term effects. However, the cumulative effect on the brain of sub-concussive hits is still poorly understood. Eighteen male collegiate student football athletes completed multi-modal MRI scans before and after a football season. We found significant changes of functional connectivity to the default-mode network, along with significant increase of cerebral blood flow both globally and at the postcentral gyrus. These changes point to the need for further investigation of the long-term development of brain networks in the presence of sub-concussive hits, and the potential relationship with brain vascular modification.