The purpose of this study was to determine whether branched-chain amino acid (BCAA) supplementation attenuates indirect indicators of muscle damage, lowers ratings of perceived exertion, and improves aerobic performance as compared to an isocaloric, carbohydrate (CHO) beverage or a non-caloric placebo beverage. Nine, untrained males (VO2 max 36.26 ± 2.23 ml/kg/min) performed three 90-minute cycling bouts at 55% VO2 max followed by a 15-minute time trial. Metabolic data was collected every 15 minutes during the steady-state ride, and indirect muscle damage markers were assessed pre, post, 4-hours, 24-hours, and 48-hours post-exercise. Pre and post-exercise concentrations of the BCAA and glucose were also recorded. All blood markers were adjusted for plasma volume shifts. There were no differences in dietary intake between trials for 3 days prior to exercise. Creatine kinase concentrations were significantly lower after the BCAA trial as compared to the placebo trial at 4, 24, and 48-hours post-exercise, as well as the CHO beverage at 24-hours post-exercise. Creatine kinase was lower in the CHO trial at the 24- and 48-hour time points as compared to the placebo trial. Lactate dehydrogenase concentrations were elevated in the placebo trial at 4-hours as compared to the BCAA trial. As compared to the alternate trials, ratings of perceived soreness were lower at 24-hours post-exercise, leg flexion torque was higher at the 48-hour time point, and plasma concentrations of the BCAA were elevated following the BCAA trial. Time-trial performance was improved in the CHO trial, and ratings of perceived exertion were lower at 75 and 90-minutes of exercise in the BCAA trial as compared to the placebo trial. There were no significant condition x time differences for leg extension torque, VO2, ventilation, heart rate, RER, or energy expenditure. In addition, there was no order effect for creatine kinase, lactate dehydrogenase, leg flexion/extension torque, ratings of perceived soreness, or time trial performance. The present data suggest that BCAA supplementation attenuates muscle damage during prolonged endurance exercise in unfit, college-aged males, but does not affect time trial performance. CHO ingestion improves time trial performance and attenuates post-exercise creatine kinase levels at 24-hours post-exercise as compared to a placebo beverage.