A fuel cell system includes a fuel cell including at least one unit cell having an anode, an anode-side flow channel for supplying a fuel to the anode, a cathode, and a cathode-side flow channel for supplying an oxidant to the cathode. The fuel cell system further includes a gas-liquid separator for catalytically purifying the effluent from the anode and the effluent from the cathode to collect liquid. The gas-liquid separator is connected to an anode-side discharge path for the effluent and a cathode-side discharge path for the effluent, which are in fluid communication with a fuel outlet of the anode-side flow channel and an oxidant outlet of the cathode-side flow channel, respectively.