Nowadays, new types of vinegar have been developed using various raw materials and biotechnological processes. The fruit of Prunus mume has been extensively distributed in East Asia and used as a folk medication for fatigue. In this study, the Prunus mume vinegar (PV) was produced by a two-step fermentation and was evaluated for its anti-fatigue activity by C2C12 myoblasts and high-intensity exercised rats. The administration of PV significantly improved running endurance and glycogen accumulation in the liver and muscle of PV supplemented rats compared to sedentary and exercised control groups. In addition, PV supplementation elicited lower fatigue-related serum biomarkers, for instance, ammonia, inorganic phosphate, and lactate. PV administered rats exhibited higher lactate dehydrogenase activity and glutathione peroxidase activity, and lower creatine kinase activity and malondialdehyde levels. Furthermore, phenolic compounds in PV were identified using HPLC analysis. The phenolic acids analyzed in PV were protocatechuic acid, syringic acid, chlorogenic acid, and its derivates. These results indicate that the administration of PV with antioxidative property contributes to the improvement of fatigue recovery in exhausted rats. The findings of this study suggest that the PV containing various bioactive constituents can be used as a functional material against fatigue caused by high-intensity exercise.