A stack for a fuel cell system, including: a membrane electrode assembly, a separator that includes a fuel passage that supplies a fuel to an anode electrode of the membrane electrode assembly and an oxidant passage that supplies an oxidant to a cathode electrode of an adjacent membrane electrode assembly, a first manifold that is formed by connecting first penetration holes that penetrate the separator in a stacking direction and that is connected to the fuel passage, a second manifold that is formed by connecting second penetration holes that penetrate the separator in the stacking direction and that is connected to the oxidant passage and a baffle that is disposed in at least one of the first manifold and the second manifold. The baffle has a membrane structure to control the fluid flow inside of the at least one of the first manifold and the second manifold.