Objectives: The purpose of this study was to examine the acute effects of branched-chain amino acids (BCAAs)-containing electrolyte beverage (AE) on water–electrolyte balance, muscle damage, time to finish the final 5 km, and muscle strength compared to a standard commercially available carbohydrate–electrolyte sports beverage (CE), pure water (W), and no rehydration (N). Methods: Fourteen trained male participants (20 ± 2 years old) completed four randomized 21 km running trials. The participants were instructed to consume their drink (150 mL W, 150 mL CE, or 150 mL AE) or no rehydration (N) at 5 km, 10 km, and 15 km. Body mass and muscle strength were assessed, and blood samples were collected before and after exercise. Perceptual scales were administered during and after running. Blood electrolyte levels (sodium, potassium, and chloride) and creatine kinase (CK) concentration were analyzed. Results: The change in plasma volume with AE was significantly smaller than that with N (p < 0.05). Consuming AE maintained the best potassium balance (p < 0.05). Twenty-four hours after exercise, serum CK concentrations significantly elevated in N, W, and CE (p < 0.05), but did not reach statistical significance in the AE group (p > 0.05). Compared to N, consuming AE resulted in significantly less soreness 24 h after exercise (p < 0.05). There was no difference in time to finish the final 5 km (p > 0.05). Maximal voluntary isometric force output was significantly lower after exercise with N and W (p < 0.05) but not with CE or AE (p > 0.05). Conclusions: Consuming a BCAAs-containing sports beverage during a 21 km run can help reduce dehydration, maintain potassium balance, lower muscle damage, and prevent the decline in lower limb strength after 21 km running.