Presently, hydrogen-fuel-cell medium-duty trucks utilize two or more modular proton exchange membrane fuel-cell stacks due to package space and economic concerns. The fuel-cell system of medium-duty trucks requires high power demand under a regular driving schedule. Since the high power demands produces significant heat generation within a very small packaging space, thermal management is crucial for maintaining the performance and long term durability of medium-duty trucks. This study was designed to investigate the various cooling configurations of dual stacks to understand the dual-stack response under thermal management conditions. A dynamic fuel-cell system model is developed to investigate the layout effect of the cooling system under load follow-up. Three different layouts of cooling system were investigated such as series cooling, parallel cooling, and two independent cooling modules with minimum cooling components. The results show that the series cooling system shows a minimum overshoot and undershoot by step change of the stack due to a cooling capacity. The cooling parasitic energy consumption is also minimized with the series cooling system