This study investigated the effects of ginseng berry extract (GBE) and its major ginsenoside Re (GinRe) on skeletal muscle atrophy and exercise performance. GBE and GinRe upregulated the mRNA expression of sirtuin1 (Sirt1) and peroxisome proliferator-activated receptor-γ coactivator-1α (Pgc-1α) in C2C12 myotubes. Administration of GBE and GinRe in high-fat diet-induced muscle atrophy mice enhanced endurance exercise performance and increased skeletal muscle weight with a significant downregulation of skeletal muscle atrophy genes and upregulation of oxidative myosin heavy chain subtypes, mitochondrial biogenesis, and oxidative phosphorylation regulatory genes in skeletal muscle tissue. Oral administration of GBE and GinRe enhanced the protein expression of SIRT1, phosphorylation of adenosine monophosphate-activated protein kinase (AMPK)/PGC-1α/peroxisome proliferator-activated receptor-δ (PPARδ) signaling axis in skeletal muscle tissue, acting as an exercise metabolism regulator. These results suggest that GBE and GinRe have the potential to enhance exercise performance through mitochondrial biogenesis.