There has been a recent call for longitudinal imaging studies to better characterize the time course of physiological recovery following sport-related concussion (SRC) and its relationship with clinical recovery. To address this, we evaluated changes to resting-state functional connectivity (rs-FC) of the whole-brain network following SRC and explored associations between rs-FC and measures of clinical outcome. High school and collegiate football athletes were enrolled during preseason. Athletes that suffered SRC (N = 62) were assessed across the acute (within 48 hr) and sub-acute (days 8, 15, and 45) phases. Matched football athletes without concussion served as controls (N = 60) and participated in similar visits. Multi-band resting-state fMRI was used to assess whole-brain rs-FC at each visit using network-based statistic and average nodal strength from regions of interest defined using a common whole-brain parcellation. Concussed athletes had elevated symptoms, psychological distress, and oculomotor, balance, and memory deficits at 48 hr postconcussion relative to controls, with diminished yet significant elevations in symptoms and psychological distress at 8 days. Both rs-FC analyses showed that concussed athletes had a global increase in connectivity at 8 days postconcussion relative to controls, with no differences at the 48-hr, 15-day, or 45-day visits. Further analysis revealed the group effect at the 8-day visit was driven by the large minority of concussed athletes still symptomatic at their visit; asymptomatic concussed athletes did not differ from controls. Findings from this large-scale, prospective study suggest whole-brain rs-FC alterations following SRC are delayed in onset but associated with the presence of self-reported symptoms.