An apparatus preventing over-cooling of a fuel cell is provided that includes a cooling fluid manifold which is mounted to a stack of the fuel cell and through which cooling fluid flows therethrough. End plates are arranged on both ends of the stack of a fuel cell, and at least one protrusion is provided on one surface of each of the end plates. The at least one protrusion is disposed inside a cooling fluid manifold to reduce the flow amount of the cooling fluid which flows in and out between the separating plates through the cooling fluid manifold.