The purpose of this study was to evaluate cardiac autonomic modulation in university athletes during the post-acute to late phase (mean, 95 days ±63) of injury at rest and during physical exertion. We also sought to evaluate the effect of time since injury and number of injuries on heart rate variability (HRV). We hypothesized that physical exertion would reveal persisting modifications in HRV following a concussion. We included, in a cross-sectional design, athletes who sustained a concussion and matched controls. Concussions were identified by a medical doctor using established criteria. Twelve male concussed and 12 control athletes took part in the study. Control participants were teammates who were chosen to match the concussed athletes with regard to their height, weight, education, and age. The beat-to-beat electrocardiogram intervals of the participants were measured at rest and during physical exertion (isometric hand grip contraction; IHGC), which was sustained for 3 minutes at 30% of the participants' maximum. Linear and nonlinear parameters of HRV were calculated. The ratio between low and high frequency (LF/HF) bands was calculated to assess the sympathovagal balance. During the IHGC, but not at rest, concussed athletes presented significantly lower power in HF bands, leading to a significantly higher LF/HF ratio (p ≤ 0.05). Thus, asymptomatic athletes still may exhibit modifications in cardiac autonomic modulation weeks to months following injury. These modifications may only become apparent during physical exertion. Monitoring HRV may aid diagnosis and provide insight about safe return to play.