The possibility to use fuel cells as an electrical power source makes them interesting for a wide range of applications. In this work, computational fluid dynamics (CFD) simulations and optical measurements are performed to predict the flow distribution in a flow setup resembling the parallel flow circuits in fuel cell stacks. For the first time it is shown that by an adaptation of the port sizes in the inlet manifold to the individual fuel cells, the average global deviation between the flow rates can be reduced from 10.1% to 4.0% by means of a model experiment. The measurements are performed with a high resolution laser Doppler velocity profile sensor (LD-PS) specifically developed for measurements in small-scale channels, in this work 4×1 mm², allowing for a spatial resolution below 2 μm and relative velocity uncertainties below 0.1%, helping to resolve installation effects possibly occurring in fuel cells to improve their efficiency. The presented results can be used by manufacturers to increase the efficiency of their fuel cell stacks.