Quercetin, a major flavonol, present abundantly in apples and onions, is widely studied for ameliorating metabolic syndrome abnormalities. However, quercetin is mainly present in plant food in the form of quercetin glycosides and has been reported for poor gastrointestinal absorption. The present study was designed with the purpose of imparting a lipophilic property to quercetin-3-O-glucoside (QG) by its acylation with eicosapentaenoic acid (EPA) and to study the influence of eicosapentaenoic acid ester of quercetin-3-O-glucoside (QE) on hyperlipidemia and inflammation in vivo and in vitro. QE was more effective in reducing the production of tumor necrosis factor-alpha (TNF-α), prostaglandin 2 (PGE2), cyclo-oxygenase (COX)-2 levels and nuclear expression of nuclear factor-kappa B (NF-кB) compared to the parent compounds (QG and EPA) and commercial drugs, after lipopolysaccharides (LPS) induced inflammation in THP-1 derived macrophages. Serum high-density lipoprotein (HDL)-cholesterol was significantly higher and hepatic total cholesterol concentration was lower in the rats fed high-fat diet supplemented with QE, compared to the high-fat diet with inflammation (HFL). The serum concentrations of C-reactive protein (CRP), interleukin (IL)-6, and interferon-gamma (IFN-γ) were significantly lower in QE treatment group than HFL group. EPA conjugated flavonol, QE, had significant anti-inflammatory and hypolipidemic properties and may be effective for the treatment of obesity-related disorders.