High levels of fats like triglycerides and cholesterol in the blood can cause cardiovascular diseases, prompting the search for safer, natural treatments. This study investigates the efficacy of Ruta chalepensis ethanol extract in lowering cholesterol levels using a rat model of hyperlipidemia induced by Triton WR-1339. Leaves and flowers of R. chalepensis were extracted with ethanol, and LC-MS analysis revealed high levels of quercetin (9.5%), 2,2-Dimethyl-3-methylidenebicyclo [2.2.1] heptane (8.1%), and other compounds, with monoterpenes being the most common class. Male Wistar rats received doses of the extract at 20 and 40 mg/kg, while fenofibrate (100 mg/kg) was the positive control. After 20 h, plasma lipid levels were significantly affected, showing a 72.1% reduction in total cholesterol for the 40 mg/kg group (p < 0.01) and a 67.6% reduction for the 20 mg/kg group (p < 0.01). High-density lipoprotein cholesterol levels decreased by 68.8% in the 40 mg/kg group (p < 0.01) and 58.6% in the 20 mg/kg group (p < 0.01). Low-density lipoprotein cholesterol saw reductions of 67.3% (p < 0.001) in the 40 mg/kg group and 60.4% (p < 0.01) in the 20 mg/kg group. Triglycerides dropped by 90.6% in the 40 mg/kg group (p < 0.001) and 86.7% in the 20 mg/kg group (p < 0.001). Overall, the results highlighted a stronger anti-hyperlipidemic effect in the 40 mg/kg group across all lipid parameters measured. The extract outperformed fenofibrate, particularly at the higher dose. These results imply that R. chalepensis extract is a promising natural alternative for managing hyperlipidemia.