A humidification apparatus for a fuel cell system is provided herein. A membrane humidifier includes humid air inlets, through which humid air discharged from a cathode of a fuel cell stack is introduced, and air outlets, through which air humidifying dry air in hollow fiber membranes is discharged, an air line connected from a cathode outlet of the fuel cell stack to the humid air inlets of the membrane humidifier to supply humid air. Exhaust lines are connected to the air outlets. A flow control valve is provided in the air line and controls the introduction of humid air into the humid air inlets, respectively. An exhaust valve is also provided to open and close flow paths of the exhaust lines. A controller controls the opening and closing of the flow control valve and the exhaust valve based on operating conditions of the fuel cell stack.