Ultra-marathon running is supposed to increase the parameters of skeletal muscle damage and impair renal function. The purpose of this study was to investigate the effect of branched-chain amino acid supplementation on skeletal muscle damage and renal function during a 100-km ultra-marathon. Twenty-eight athletes were randomly divided into two groups, one group using branched-chain amino acid supplementation (BCAA) and a control group (CON). The athletes in the BCAA group were supplemented with a total of 50 g of an amino acid concentrate including 20 g of BCAA. The intake of energy, antioxidants and parameters of both skeletal muscle damage and renal function were determined. Race time was not different between BCAA and CON when controlled for the personal best time in a 100-km ultra-marathon. Neither the intake of energy and antioxidants nor the parameters of skeletal muscle damage and renal function were different between BCAA and CON. We concluded that BCAA-supplementation before and during a 100-km ultra-marathon had no effect on performance, skeletal muscle damage or renal function.