Atherosclerosis is caused by inflammatory processes that alter the permeability of arterial wall cells and leucocyte recruitment, leading to oxidation of low-density lipoproteins in the artery. The use of dietary polyphenols as antioxidants seems promising. Herein, molecular docking-based screening was initially used to predict the interactions of epicatechin and hydroxytyrosol on multiple cytokines that can trigger atherosclerosis development. Computational results show that epicatechin and hydroxytyrosol interact with the cytokines, namely, intercellular adhesion molecule-1, vascular cell adhesion molecule-1, monocyte chemoattractant protein 1 (MCP-1), granulocyte-macrophage colony-stimulating factor, leukocyte differentiation antigen CD36, and oxidized low-density lipoprotein receptor-1. Cytotoxicity of both the bioactive compounds to human monocytic THP-1 macrophages was evaluated by lactate dehydrogenase and crystal violet assays. ROS activity evaluation was done for the phytocompounds followed by monocyte migration assay for MCP-1. The expression levels of selected biomarkers were further assessed by quantitative polymerase chain reaction. Inhibition of these atherosclerotic biomarkers may limit the atherogenic effect. Notably, these two polyphenols at a concentration of 0-125 µg/mL for 24 h showed no cytotoxicity on THP-1 macrophages and exhibited decreased ROS production and MCP-1 levels. The genes implicated in the early stages of inflammation are potential therapeutic targets to effectively reduce atherogenesis and prevent CVD. The interaction between the selected cytokines and the two natural compounds indicates their potential ability to inhibit the inflammation in vitro and exhibit anti-atherogenic effects. Hence, epicatechin and hydroxytyrosol possess significant anti-atherosclerotic effects and, in combination, could contribute positively to the treatment of atherosclerosis.