The present study evaluated the effects of acid-treated rutin on hyperlipidemia and obesity in high-fat diet (HFD)-induced obese mice. The mice consumed a HFD with or without acid-treated rutin for 7 weeks. Body weight gain considerably decreased, by approximately 33%, in the acid-treated rutin (AR) and quercetin (Q) groups compared to that in the HFD group. The adipocytes’ size in epididymal fat in AR and Q groups was significantly reduced compared to that in the HFD group (p < 0.05). Treatment with AR decreased the levels of triglycerides, total cholesterol, and low-density lipoprotein cholesterol compared to the HFD group. In particular, administration of AR significantly decreased serum triglyceride (36.82 mg/dL) by 46% compared to HFD (69.30 mg/dL). The AR group also showed significantly decreased atherogenic indices and cardiac risk factors. These results suggest that deglycosylated rutin generated by acid treatment enhances the anti-obesity and hypolipidemic effects in obese mice, and provides valuable information for improving the functional properties of glycosidic flavonoids.