Whey protein has been widely applied to athletes and the fitness field for muscle growth and performance improvement. Limited studies focused on the beneficial effects of whey on aerobic exercise according to biochemical assessments. In the current study, 12 elite male track runners were randomly assigned to whey and maltodextrin groups for 5 weeks' supplementation. The aim of this study was to investigate the effect of whey protein on physiological adaptions and exercise performance. During this period, three time points (pre-, post-, and end-test) were used to evaluate related biochemical parameters, body composition, and performance. The post-test was set 1 day after a marathon for injury status evaluation and the end-test was also assessed after 1-week recovery from endurance test. The results showed that the whey group exhibited significantly lower aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, and creatine kinase indicators after the marathon (post-test), as well as at the end-test (p<0.016). The endurance performance in twelve-minute walk/run was also significantly elevated (p<0.012) possibly due to an increase in the muscle mass and amelioration of exercise injuries. In the current study, we demonstrated that whey protein can also be used for aerobic exercise for better physiological adaptation, in addition to resistance training. Whey protein could be also a potential nutrient supplement with a variety of benefits for amateur runners.