Abstract The flow distribution issue is of significance to the fuel cell stack performance and durability, which herein is studied from a theoretical and practical level. The manifold flow fundamentals are clarified and the pressure‐reconstruction‐based principle to regulate flow distribution is revealed. The prerequisite and corequisite lie in the ratio of pressure drop between headers and the entire manifold, and the pressure recovery in the inlet header. Accordingly, a step‐by‐step manifold design methodology is proposed and further quantified by detailed and organized simulations. A desirable effect on flow uniformity is validated in large‐scale stacks consisting of 300 and 400 cells, and the values of flow uniformity index represented by coefficient of variation ( CV ) are 3.32% and 2.95%, respectively. Moreover, a novel wedge‐shaped layout of the intake header is proposed for further optimization. The corresponding CV values have notably declined to 1.36% and 1.29%, nearly 60% lower than the conventional rectangular counterparts.