A fuel cell system includes a fuel cell stack having a membrane electrode assembly and an internal reactant gas passage, a unit that detects or estimates an actual retained water quantity (R.W.Q.), and a power generation control unit having a normal-time mode, a normal-time drying mode and a stop-time drying mode. In the normal-time drying mode, the fuel cell stack is caused to generate electric power while being dried more than in the normal-time mode until the actual R.W.Q. is decreased to a target R.W.Q. In the stop-time drying mode, when the actual R.W.Q. is equal to or more than a flooding threshold at a time of detection of a system stop instruction, the fuel cell stack is caused to generate electric power while being dried more than in the normal-time drying mode until the actual R.W.Q. is decreased to a target R.W.Q.