Atherosclerosis is the devastating underlying cause of cardiovascular disease and it preferentially develops at arterial regions exposed to disturbed flow (DF), while much less at regions of unidirectional laminar flow (UF). Recent studies have demonstrated that DF and UF differentially regulate important aspects of endothelial function, such as vascular inflammation, oxidative stress, vascular tone, cell proliferation, senescence, mitochondrial function, and glucose metabolism. DF and UF regulate vascular pathophysiology via differential regulation of mechanosensitive transcription factors (MSTFs) (KLF2, KLF4, NRF2, YAP/TAZ/TEAD, HIF-1α, NF-κB, AP-1 and others). Emerging studies show that MSTFs represent promising therapeutic targets for the prevention and treatment of atherosclerosis. Here, we present a comprehensive overview of the role of MSTFs in atherosclerosis and highlight future directions for developing novel therapeutic agents by targeting MSTFs.