Atherosclerosis is a chronic condition marked by lipid accumulation, inflammation, and endothelial dysfunction, leading to narrowed arteries and an increased risk of heart attacks and strokes. Key proteins involved in this process include PCSK9, LOX-1, ROS, CD36, and ABCA1. PCSK9 degrades LDL receptors, raising blood LDL levels, while LOX-1 and CD36 promote the uptake of oxidized LDL by macrophages, enhancing foam cell formation. ABCA1, on the other hand, facilitates cholesterol efflux to HDL, reducing atherosclerosis risk. Red watermelon (Citrullus lanatus), rich in lycopene, citrulline, and vitamins A, C, and E, has antioxidant and cardioprotective properties. This study aimed to explore the effects of red watermelon extract on the expression of PCSK9, LOX-1, ROS, TNFα, CD36, and ABCA1 in a Wistar rat model of atherosclerosis. In a randomized control trial, male Wistar rats were induced with a high-fat diet (margarine) and treated with red watermelon extract for four weeks. The findings showed that red watermelon extract reduced the expression of PCSK9, LOX-1, CD36, ROS, and TNFα, leading to lower LDL levels, and inhibited foam cell formation. It also increased ABCA1 expression, thus promoting cholesterol efflux and higher HDL levels. Path analysis confirmed that the anti-atherogenic effect of C. lanatus was primarily mediated through the PCSK9-ABCA1-FC axis. This suggests that red watermelon may serve as a natural agent for atherosclerosis prevention by regulating lipid metabolism pathways.