Psacalium decompositum, commonly known as “Matarique,” is a medicinal plant used in Mexico for diabetes mellitus empirical therapy. Previous studies have shown that the fructooligosaccharides (FOS) present in the roots of this plant exhibit a notable hypoglycemic effect in animal models; this effect might be associated with the attenuation of the inflammatory process and other metabolic disorders. In this study, we examined the effects of FOS fraction administration in a fructose-fed rat model for obesity. Phytochemical chromatographic studies (high performance thin layer chromatography and nuclear magnetic resonance) were performed to verify isolation of FOS. 24 male Wistar rats were maintained for 12 weeks on a diet of 20% HFCS in drinking water and chow. Glucose, cholesterol, triglycerides and liver transaminases levels were measured monthly, after administering FOS fraction intragastrically (150 mg/kg/day for 12 weeks), while the levels of inflammatory cytokines were only quantified at the end of the treatments. Rats treated with FOS fraction decreased body weight, cholesterol, triglycerides, and significantly reduced IL-6, IFN-γ, MCP-1, IL-1β and VEGF levels (p < 0.05). These results suggest that P. decompositum has anti-inflammatory and hypolipidemic properties that might be used as an alternative treatment for the control of obesity.