The purpose of this study was to evaluate cardio-autonomic regulation in adolescent athletes with and without history of concussion, at rest and following moderate intensity aerobic exercise. We hypothesized that exercise would reveal covert impairments in cardio-autonomic function for athletes with a history of concussion following aerobic exercise. Male adolescent hockey players were recruited and divided into history of diagnosed concussion and matched controls without history of concussion. Athletes in the concussion group were 3 + months from injury, asymptomatic, and currently engaged in sport. Cardio-autonomic function was measured for 5-minute at rest, and for 10-minute following cycle ergometery at 60%–70% theoretical maximal heart rate. Variable evaluated were mean normal-normal interval (mean NN), standard deviation of NN intervals (NN), root mean square of successive differences (RMSSD), low frequency (LF), high frequency (HF) and approximate entropy (ApEn). No differences were observed between those with and without a history of concussion at rest. However, the concussion group showed significant differences in mean RR interval and approximate entropy following exercise relative to matched controls (p = 0.05). Moderate intensity exercise may induce cardio-autonomic dysfunction in adolescent athletes with a history of concussion, even after they are asymptomatic and make a full return to play. These findings support prior reported findings that exercise can induce a decoupling between the autonomic and cardiovascular systems following concussion.