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Objective: The aim of this pilot cohort study was to examine changes in the organization of resting-state brain networks in high school football athletes and its relationship to exposure to on-field head impacts over the course of a single season. Methods: Seventeen male high school football players underwent functional magnetic resonance imaging and computerized neurocognitive testing (CNS Vital Signs) before the start of contact practices and again after the conclusion of the season. The players were equipped with helmet accelerometer systems (Head Impact Telemetry System) to record head impacts in practices and games. Graph theory analysis was applied to study intranetwork local efficiency and strength of connectivity within six anatomically defined brain networks. Results: We observed a significant decrease in the local efficiency (−24.9 ± 51.4%, r = 0.7, p < 0.01) and strength (−14.5 ± 26.8%, r = 0.5, p < 0.01) of functional connectivity within the frontal lobe resting-state network and strength within the parietal lobe resting-state network (−7.5 ± 17.3%, r = 0.1, p < 0.01), as well as a concomitant increase in the local efficiency (+55.0 +/- 59.8%, r = 0.5, p < 0.01) and strength (+47.4 +/- 47.3%, r = 0.5, p < 0.01) within the mediotemporal networks. These alterations in network organization were associated with changes in performance on verbal memory (p < 0.05) and executive function (p < 0.05). We did not observe a significant relationship between the frequency or cumulative magnitude of impacts sustained during the season and neurocognitive or imaging outcomes (p > 0.05). Conclusion: Our findings suggest the efficiency and strength of resting-state networks are altered across a season of high school football, but the association of exposure levels to subconcussive impacts is unclear. Advances in knowledge: The efficiency of resting-state networks is dynamic in high school football athletes; such changes may be related to impacts sustained during the season, though further study is needed.