There are provided a hydrogen production apparatus and a hydrogen producing method that can easily bring the temperature of a gas to be supplied to a preferential oxidation catalyst bed to a proper range without the necessity of flow rate control of a cooling medium, and a fuel cell system which is relatively inexpensive and can easily realize stable operation. The hydrogen producing method includes a reforming step of obtaining a hydrogen-containing gas from a raw material for hydrogen production by utilizing a reforming reaction, a shift reaction step of reducing the concentration of carbon monoxide in the gas obtained from the reforming step by a shift reaction, a cooling step of cooling the gas obtained from the shift reaction step, a heating step of heating the gas cooled in the cooling step and a preferential oxidation reaction step of reducing the concentration of carbon monoxide in the gas heated in the heating step, wherein in the heating step, the gas cooled in the cooling step is heated by heat exchange with the use of heat generated by the preferential oxidation reaction. A hydrogen production apparatus suitable for implementing this method. A fuel cell system provided with the hydrogen production apparatus.