A system for estimating the amount of purge of a fuel cell is provided. The system includes a fuel cell that generates power by receiving hydrogen at an anode side and receives oxygen at a cathode side. A recirculation line is connected with the anode side of the fuel cell, and the gas included hydrogen therein is circulated in the recirculation line. A flow amount estimator estimates the flow amount of gas inside the recirculation line. A purge valve is positioned in the recirculation line and discharges the gas in the recirculation line to the outside when opened. A purge amount estimator estimates the amount of purge for each gas discharged through the purge valve by reflecting the flow amount of the gas estimated by the flow amount estimator.