We describe a piezoelectric pumping system for studying the mechanobiology of human aortic endothelial cells (HAECs) under pulsatile flow in microfluidic structures. The system takes advantage of commercially available components, including pumps, flow sensors, and microfluidic channels, which can be easily integrated, programmed, and operated by cellular biologists. Proof-of-concept experiments were performed to elucidate the complex mechanotransduction processes of endothelial cells to pulsatile flow. In particular, we investigated the effect of atheroprone and atheroprotective pulsatile shear stress on endothelial cytoskeleton remodeling and distribution of β-catenin, as well as nuclear shape and size. The system is simple to operate, relatively inexpensive, portable, and controllable, providing opportunities for studying the mechanobiology of endothelial cells using microfluidic technologies.