A hydrogen generation system comprising: a reformer configured for generating a hydrogen-containing gas using a raw material and reforming water; a combustor configured for combusting the hydrogen-containing gas generated by the reformer and air to generate an exhaust gas; an exhaust gas channel configured for flowing the exhaust gas therethrough; a cooling water channel configured for flowing cooling water therethrough in order to cool the exhaust gas; a condenser configured for causing moisture within the exhaust gas to be condensed by heat exchange between the exhaust gas and the cooling water to generate condensed water; a water tank configured for accumulating, as the cooling water, the condensed water generated in the condenser; a water supply pump configured for causing the cooling water accumulated inside the water tank to be supplied to the condenser; a reforming water channel which branches at a first branching part provided between the water supply pump and the condenser in the cooling water channel, and configured for flowing a portion of the cooling water therethrough to the reformer as the reforming water; a heater which is provided further downstream than the first branching part in a flow direction of the cooling water in the cooling water channel, and configured for heating the cooling water channel; a first temperature detector configured for detecting a temperature of the cooling water channel heated by the heater; and a controller, wherein, in an activation operation mode which is an operation mode from activation to steady operation of the hydrogen generation system, the controller is configured for causing the heater to operate, and determining whether or not inside of the reforming water channel is filled with the reforming water, based on the temperature detected by the first temperature detector after the heater has operated. a reformer configured for generating a hydrogen-containing gas using a raw material and reforming water; a combustor configured for combusting the hydrogen-containing gas generated by the reformer and air to generate an exhaust gas; an exhaust gas channel configured for flowing the exhaust gas therethrough; a cooling water channel configured for flowing cooling water therethrough in order to cool the exhaust gas; a condenser configured for causing moisture within the exhaust gas to be condensed by heat exchange between the exhaust gas and the cooling water to generate condensed water; a water tank configured for accumulating, as the cooling water, the condensed water generated in the condenser; a water supply pump configured for causing the cooling water accumulated inside the water tank to be supplied to the condenser; a reforming water channel which branches at a first branching part provided between the water supply pump and the condenser in the cooling water channel, and configured for flowing a portion of the cooling water therethrough to the reformer as the reforming water; a heater which is provided further downstream than the first branching part in a flow direction of the cooling water in the cooling water channel, and configured for heating the cooling water channel; a first temperature detector configured for detecting a temperature of the cooling water channel heated by the heater; and a controller, wherein, in an activation operation mode which is an operation mode from activation to steady operation of the hydrogen generation system, the controller is configured for causing the heater to operate, and determining whether or not inside of the reforming water channel is filled with the reforming water, based on the temperature detected by the first temperature detector after the heater has operated.