A preferential oxidation reactor for removing carbon monoxide in a hydrogen mixture gas is disclosed. The preferential oxidation reactor may include a housing having a catalytic layer provided therein, a mixture gas supply portion inserted into the interior of the housing and penetrating the catalytic layer, a condensate receiving portion contained within the housing and in fluid communication with a gas outlet port of the mixture gas supply portion and condensate control tubes arranged in the catalytic layer of the housing and in fluid communication with the condensate receiving portion. The condensate control tubes may have a capillary structure. A fuel cell system including the preferential oxidation reactor is also disclosed.