Clausena excavata (C. excavata) has been used as a traditional medicine for the treatment of abdominal pain, enteritis, dysentery, and malaria. The present study was designed to evaluate the effect of a 50% ethanol extract of C. excavata (ECE) on weight loss, adipocyte size, and obesity-related biochemical parameters in high-fat diet (HFD)-induced obese mice. After 6 weeks of HFD + ECE administration, HFD-induced total fat, subcutaneous fat, and visceral fat were evaluated by micro-computed tomography. The serum levels of triglyceride (TG), total cholesterol (TCH), high-density lipoprotein (HDL) cholesterol, and low-density lipoprotein (LDL) cholesterol were evaluated with a biochemical analyzer, and leptin and adiponectin levels in the serum were assessed via enzyme-linked immunoassay (ELISA). Moreover, adipocyte size and lipid formation in the liver were examined. We found that weight gain, epididymal fat pad weight, adipocyte size, and lipid formation were markedly attenuated in the livers of HFD-induced obese mice treated with ECE. Furthermore, TG, TCH, and leptin decreased in the serum, whereas adiponectin increased. In conclusion, our data show that ECE has potent anti-obesity activity in vivo and support the development of ECE as a potential therapeutic agent for the treatment of obesity.