A fuel cell system for generating power by supplying anode gas and cathode gas to a fuel cell, comprising: a compressor for supplying the cathode gas to the fuel cell; a first target pressure setting unit (4, S2) setting a first target pressure of the cathode gas based on a request of the fuel cell; and a pulsating operation unit causing a pressure of the anode gas to pulsate between an upper limit target pressure in pulsation and a lower limit target pressure in pulsation set based on an operation state of the fuel cell system, characterized by further comprising: a second target pressure setting unit (4, S2) setting a second target pressure of the cathode gas for keeping a differential pressure in the fuel cell to be within a permissible differential pressure range according to the pressure of the anode gas in the fuel cell, the permissible differential pressure range being defined so as to protect an electrolyte membrane of the fuel cell; and a compressor control unit (4, 114) controlling the compressor based on the higher pressure of the first target pressure and the second target pressure, wherein the second target pressure setting unit (4, S2) sets the second target pressure to a pressure obtained by subtracting the permissible differential pressure from the upper limit target pressure in pulsation. a compressor for supplying the cathode gas to the fuel cell; a first target pressure setting unit (4, S2) setting a first target pressure of the cathode gas based on a request of the fuel cell; and a pulsating operation unit causing a pressure of the anode gas to pulsate between an upper limit target pressure in pulsation and a lower limit target pressure in pulsation set based on an operation state of the fuel cell system, characterized by further comprising: a second target pressure setting unit (4, S2) setting a second target pressure of the cathode gas for keeping a differential pressure in the fuel cell to be within a permissible differential pressure range according to the pressure of the anode gas in the fuel cell, the permissible differential pressure range being defined so as to protect an electrolyte membrane of the fuel cell; and a compressor control unit (4, 114) controlling the compressor based on the higher pressure of the first target pressure and the second target pressure, wherein the second target pressure setting unit (4, S2) sets the second target pressure to a pressure obtained by subtracting the permissible differential pressure from the upper limit target pressure in pulsation. a second target pressure setting unit (4, S2) setting a second target pressure of the cathode gas for keeping a differential pressure in the fuel cell to be within a permissible differential pressure range according to the pressure of the anode gas in the fuel cell, the permissible differential pressure range being defined so as to protect an electrolyte membrane of the fuel cell; and a compressor control unit (4, 114) controlling the compressor based on the higher pressure of the first target pressure and the second target pressure, wherein the second target pressure setting unit (4, S2) sets the second target pressure to a pressure obtained by subtracting the permissible differential pressure from the upper limit target pressure in pulsation.