A fuel cell system 100 includes a fuel cell 10, a cathode gas supply system 30, a supply valve 34, an exhaust valve 43 and a controller 20. The fuel cell 10 has a supply manifold M1, an exhaust manifold M2, and a power generation area GA connected with these manifolds M1 and M2. The cathode gas supply system 30 causes a gas to be flowed into the supply manifold M1. The supply valve 34 is operable to seal the supply manifold M1, whereas the exhaust valve 43 is operable to seal the exhaust manifold M2. The controller 20 closes the supply valve 34 and the exhaust valve 43 after operation stop of the fuel cell 10 to seal the fuel cell 10 under a specified pressure and then waits for a predefined time. The controller 20 subsequently opens the supply valve 34 to move water remaining in the power generation area GA on the flow of the gas toward outside of the power generation area GA.