A hydrogen generation apparatus includes: a reformer configured to generate a hydrogen-containing gas by using a raw material; a hydrodesulfurizer configured to remove a sulfur compound from the raw material; a recycle passage through which the hydrogen-containing gas is supplied to the hydrodesulfurizer; a condenser provided on the recycle passage or on a gas passage upstream from the recycle passage; a drain passage through which water condensed in the condenser is drained; a heating medium passage through which a heating medium that recovers heat from the condenser flows; a delivery device configured to cause the heating medium to flow through the heating medium passage; and a controller configured to cause the delivery device to operate when the hydrogen-containing gas is not flowing through the recycle passage at at least one of start-up and stopping of the hydrogen generation apparatus.