Gambejaeseup-tang (GBJST) have recently been used as an anti-obesity herbal medicine but their effect and mechanism of action have not been studied. We modified ingredients of GBJST based on the previous experiments about exploring herbs to suppress triglyceride accumulation in 3T3-L1 adipocytes. We investigated the effects of modified GBJST on energy, glucose and lipid homeostasis using female rats with diet-induced obesity and their action mechanism was also determined. Rats fed a high-fat diet (HFD) were divided into 3 groups: rats in each group received 0.2 or 2 g water extracts of modified GBJST (L-GBJST or H-GBJST) or 2 g cellulose per kg body weight (a negative control) on a daily basis. A further group was fed a low-fat diet (LFD) as a positive control. We found that modified GBJST dose-dependently decreased body weight and mesenteric and retroperitoneal fat more than the control. This decrease was due to the reduction in energy intake and the increase of energy expenditure. HFD increased fat oxidation more than LFD and modified GBJST further increased fat oxidation as a major energy source more than the control in a dose-dependent manner. In addition, H-GBJST improved glucose tolerance without changing serum insulin levels during an oral glucose tolerance test. H-GBJST also suppressed the increase of serum total and LDL cholesterol and triglyceride levels by HFD. In conclusion, modified GBJST have a good anti-obesity effect by decreasing energy intake and increasing energy expenditure mainly as fat in female rats with diet-induced obesity. It also improves glucose tolerance and lipid metabolism.