Post-exercise whey protein isolate (WPI) supplement is beneficial for skeletal muscle recovery due to the stimulation of branched chain amino acids (BCAAs). This implies us that intake slow digestion rate of protein to sustain BCAAs releasing rate may facilitate muscle protein synthesis. To examine this hypothesis, we conducted a series of protein supplements including modified slow-digesting whey (SDW), whey, hydrolyzed whey and casein, orally to mice undergoing endurance running. Our results showed that the SDW gavage constant supplied BCAAs in the serum of mice within 6 h and significantly enhanced (P < 0.01) endurance exercise capacity, compared to other groups. In addition, the SDW supplementation increased the cross-sectional area of mice gastrocnemius fibers, as well as their muscle and liver glycogen content. It also increased the testosterone/cortisol ratio in serum and interleukin-6 (IL-6) levels in muscle, while it decreased the tumor necrosis factor-alpha (TNF-α) levels and oxidative stress in muscle. Moreover, it may activate mechanistic target of rapamycin signaling by upregulating mRNA (bcat-1 and pgc-1α) expression. Thus, our findings illustrate that prolonged BCAAs supply duration promotes mice endurance running capacity and skeletal muscle growth, contributing to the advancement of sports nutrition practices.