Obesity is a growing health problem and a significant contributor to the global burden of disease. Statins have shown efficacy in modulating the mortality risk associated with obesity. Myrrh has recently been proven to reduce body weight gain and improve lipid profiles in obese hyperlipidemic rats. The aim of this study was to formulate and evaluate the anti-obesity potential of a myrrh oil-based nanoemulsion containing the hypolipidemic agent, atorvastatin. A two-factor, three-level, full factorial design was adopted to formulate and optimize the nanoemulsion formulations. The prepared formulations were characterized in terms of drug-excipient compatibility studies, physical appearance, rheological behavior, in vitro drug release, stability, and in vivo anti-obesity potential. The prepared nanoemulsion formulations showed a uniform size distribution with a droplet size within the nano-size range. The release of drug from the nanoemulsion formulations was dependent on the surfactant concentration used. Interestingly, all developed nanoemulsions were stable for up to 3 months upon storage at refrigerator and room temperature. Most importantly, in the high-fat diet-induced obesity rat model, addition of myrrh oil to oleic acid as an oily phase for nanoemulsion showed a synergistic effect to the anti-obesity potential of the hypolipidemic drug atorvastatin. In conclusion, formulating atorvastatin into a myrrh oil-based nanoemulsion might represent a promising approach for augmenting the anti-obesity action of atorvastatin, not only by enhancing its systemic bioavailability, but also by gaining the benefit of the synergistic anti-obesity effect of myrrh oil.