A fuel cell system capable of computing fuel level stored in a fuel tank, and more particularly to a fuel cell system capable of computing fuel level without using a flux sensor or flow rate sensor includes: a fuel tank storing fuel; a stack for generating electricity by the electro-chemical reaction of the fuel; a fuel pump for transferring fuel from the fuel tank to the stack; a fuel pump for transferring the fuel from the fuel tank to the stack; a pumping controller for generating a pump control signal controlling the pumping operation of the fuel pump; and a fuel level computing unit for computing the amount of fuel used and fuel level from the waveform of the pump control signal. In some embodiments, the fuel cell system informs a user when the fuel level is low, with reduced manufacturing costs.