The influence of yerba mate extract (YME) and two concentrated fractions of methylxanthines–polyphenols (MXPL) and saponins (SFL) from yerba mate on the lipid metabolism of Wistar rats fed with a high-fat diet were examined. A Box–Behnken design was employed for the optimization of yerba mate extraction. Subsequently, one-step separation using solid phase fractionation was applied. HPLC–PDA and UPLC/Q-TOF-MS were used for quantification and identification of the main compounds. YME induced reductions on intra-abdominal fat weight gain and LDL plasma level. MXPL decreased plasma levels of cholesterol, LDL and triacylglycerols. In addition, this fraction increased lipogenesis of the muscle, hepatic glycogen synthesis and lipolysis in adipose tissue. SFL enhanced lipogenesis in adipose tissue and also fecal fat excretion comparing to both controls. Moreover, all mate preparations could entirely revert the hepatic lipogenesis induced by the high-fat diet. Thus, the yerba mate extract and fractions exhibited a potential anti-obesity effect on lipid metabolism of the Wistar rat and deserve further investigation.