A hydrogen supply control system for a fuel cell is provided. The system includes a fuel cell stack that generates electricity using supplied hydrogen and air and a recirculation line that supplies hydrogen discharged from an outlet of the fuel cell stack back to an inlet of the fuel cell stack. A purge valve is disposed at an outlet side of the fuel cell stack of the recirculation line and discharges hydrogen in the recirculation line to the outside as the outlet is opened. A recirculation determining processor determines a recirculation state of the recirculation line and a concentration estimator estimates a purge amount for each gas, which is purged by the purge valve, based on the determined recirculation state and estimates a concentration of hydrogen in the recirculation line based on the estimated purge amount for each gas.