A manifold assembly for use with a fuel cell stack for the purpose of ensuring a desired flow distribution to fuel cells within the stack, with the most commonly desired being uniform flow distribution. Said manifold assembly comprising: an external manifold for abutting and sealingly enclosing a face of the fuel cell stack, wherein the manifold comprises an enclosure for one of: providing inlet gas to the fuel cell stack and receiving exhaust gas from said fuel cell stack; and one or more baffles disposed in the enclosure of the external manifold, the one or more baffles one of: (a) controlling gas flow distribution and direction of the inlet gas from the enclosure to fuel cells of the fuel cell stack to achieve a predetermined distribution or a uniform distribution; and (b) controlling gas flow distribution of the exhaust gas flow within the enclosure to achieve the predetermined distribution or the uniform distribution of gas to fuel cells of the fuel cell stack. A multi-stack fuel cell system including a baffling assembly with one or more baffles for providing a predetermined gas flow distribution to each fuel cell stack in the fuel cell system is also described. The baffling assembly is provided at a system level and comprises one or more baffles in an intake assembly and/or in an exhaust assembly of the multi-stack fuel cell system, so that each fuel cell stack receives a predetermined amount of gas.