CONTEXT: After a sport-related concussion, many athletes experience persisting neurophysiological alterations. These alterations may be absent at rest but emerge during moments of physiological stress. Unnoticed and untreated neurophysiological dysfunction may negatively affect long-term neurologic health in adolescent athletes, as they are at a critical point in development. OBJECTIVE: To assess cardio-autonomic functioning in athletes with and those without a history of concussion by quantifying measures of heart rate variability (HRV) during times of physical and mental exertion. DESIGN: Case-control study. SETTING: Research laboratory. PATIENTS OR OTHER PARTICIPANTS: Thirty-four male Hockey Quebec Midget-AAA hockey players were separated into those with (n = 16; age = 16.06 +/- 0.73 years, body mass index = 23.29 +/- 1.79) and those without (n = 18; age = 15.98 +/- 0.62 years, body mass index = 23.60 +/- 2.49) a history of concussion. INTERVENTION(S): All athletes underwent a series of HRV recording sessions (1) at rest, (2) while completing a cognitive task at rest, and (3) while completing a cognitive task after a bout of submaximal aerobic exercise. MAIN OUTCOME MEASURE(S): Time-domain measures of HRV, including mean NN intervals, SD of NN intervals, and root mean square of successive NN interval differences, were quantified for each assessment. RESULTS: No differences in characteristics were evident between groups. No between-groups differences in HRV at rest were observed. However, during the cognitive task at rest and after aerobic exercise, athletes with a history of concussion demonstrated a higher SD of NN intervals (78.1 +/- 4.3 versus 63.2 +/- 4.1 milliseconds and 71.2 +/- 4.3 versus 65.2 +/- 3.8 milliseconds, respectively; F1,31 = 4.31, P = .046) and root mean square of successive NN interval differences (75.8 +/- 6.0 versus 59.0 +/- 5.6 milliseconds and 74.0 +/- 5.5 versus 59.0 +/- 5.2 milliseconds, respectively; F1,31 = 4.88, P = .04) than athletes without a history of concussion. CONCLUSIONS: Concussive injuries may result in long-term cardio-autonomic dysfunction. These deficits may not be present at rest but may be triggered by physiological stress.