Atherogenic dyslipidemia is a condition and responsible for the induction of major cardiovascular diseases. Traditionally, Nepeta hindostana a medicinal plant commonly used as cardioprotective in Indo-Pak regions has gained importance because of its therapeutic active flavonoid Nepitrin-7-O-glucoside. Flavonoid-glycosides are steroids having the ability to exert specific, decisive action on the cardiac muscle. In the present research work flavonoid, Nepitrin-7-O-glucoside was isolated from methanolic extract via chromatographic techniques. The structure was elucidated and confirmed by different spectral techniques like Mass and 1H NMR spectrometry. Various preclinical atherosclerosis parameters such as lipid levels, SGOT/SGPT, body weight, histology of aorta and heart were estimated and beneficial effect of Nepitrin in high-fat diet (HFD) induced atherosclerosis for six weeks were observed. Outcomes of the preclinical results showed and proved that Nepitrin significantly improved dyslipidemia at an effective dose of 50 mg/kg as compared with HFD control and Simvastatin. Molecular docking showed significant binding affinity towards the target PPAR-α receptor (PDB: 2P54). Further the docked ligands with PDB: 2P54 were exposed to molecular dynamics studies to confirm the dynamic behaviour of PPAR-α receptor. Outcomes of the results of the in-vivo study and molecular dynamics study were in correlation with each-others. Further, it can be concluded that Nepitrin has a potent antiatherogenic agent and act by reducing the lipid levels via acting on PPAR-α receptor and regenerating the damaged cells. Copyright © 2020 Elsevier Inc. All rights reserved.