Abstract Background Thymus atlanticus is an endemic plant of the Mediterranean region, which has been used in the Moroccan mountain area to treat several diseases. This study aimed to investigate the effect of polyphenol, flavonoid, and saponin fractions derived from this plant on acute and chronic hyperlipidemia in male albino mice. Results The results indicated that the injection of Triton WR-1339 (20 mg/100 g body weight (B.wt.)) and 6-week administration of a high-fat diet (which is an 81.8% standard diet supplemented with 2% cholesterol, 16% lard, and 0.2% cholic acid) significantly increased plasma total cholesterol, triglycerides and low-density lipoprotein cholesterol (LDL-C), but did not affect high-density lipoprotein cholesterol (HDL-C) levels in mice. Administration of a single dose (2 mg/kg B.wt.) of polyphenol, flavonoid, or saponin fractions significantly suppressed the effect of Triton injection on plasma total cholesterol, triglycerides, and LDL-C. In addition, the supplementation of the high-fat diet with polyphenol fraction (2 mg/kg B.wt./day) prevented the increase of total cholesterol, triglycerides, and LDL-C, and effectively increased HDL-C level when compared to mice feeding only the high-fat diet. Conclusion In conclusion, phenolic compounds from Thymus atlanticus possess a significant hypocholesterolemic and hypotriglyceridemic effects and, therefore, could have an important role in the management of dyslipidemia.