Demands for anthocyanins are steadily growing due to their positive bioactivities in human health and food coloration. This study was performed to evaluate the characteristics of purified purple passion fruit epicarp anthocyanins (PFEA) as well as its anti-fatigue activity and underlying mechanisms in mice. The result showed that three major anthocyanins including cyanidin-3-O-glucoside, cyanidin-3-O-rutinoside and peonidin-3-O-glucoside were identified, and the total content of these anthocyanins was 710.40 mg/g in PFEA. PFEA significantly prolonged the weight-loaded forced swimming time, decreased lactate dehydrogenase (LDH), the blood lactate (BLA) and the blood urea nitrogen (BUN) levels, and increased the liver glycogen (LG) content. Meanwhile, PFEA could ameliorate fluctuates in oxidative stress biomarkers (MDA), antioxidant enzymes (SOD) and inflammatory cytokines (TNF-α, IL-1β, IL-6). Moreover, the mRNA expression of PGC-1α and PPARα in skeletal muscles were also up-regulated by PFEA treatment. In conclusion, these results showed that supplementing PFEA could relieve fatigue effects.