Quercetin has been demonstrated to be effective in increasing physical endurance in mice and humans. However, the mechanisms involved are not fully understood. In this study, male Kunming mice were fed a diet containing 0.1% quercetin for 14 days before swimming for 60 min. The overall serum metabolic profile was investigated by a ¹H nuclear magnetic resonance-based metabolomic approach. Serum glucose, lactate, nonesterified fatty acids (NEFA), and nonprotein nitrogen (NPN), as well as hepatic and muscular glycogen were measured biochemically. The results of metabolomic analysis showed that swimming induced a significant change in serum metabolic profile. Relative increases in the levels of lactate, alanine, low-density lipoprotein-very low-density lipoprotein, and unsaturated fatty acids, and decreases in choline, phosphocholine, and glucose were observed after swimming. With quercetin supplementation, these changes were attenuated. The results of biochemical assays were consistent with the data obtained from metabolomic analysis, in that serum NEFA was increased while lactate and NPN decreased after exposed to quercetin in swimming mice. Similar change in NEFA was also found in liver and gastrocnemius muscle tissues. Our current findings suggest that quercetin alters energy metabolism in swimming mice and increased lipolysis may contribute to the actions of quercetin on physical endurance.