There are disclosed a selective permeation membrane reactor (10) which includes a selective permeation membrane (31) having an excellent permeation performance and a separation performance with suppresses of methanation reaction of CO 2 contained in hydrogen-containing gas to efficiently perform CO methanation reaction and manufacture highly pure hydrogen, and a method of manufacturing a hydrogen gas. The selective permeation membrane reactor includes a CO reducing unit for reducing carbon monoxide contained in concentrated hydrogen-containing gas; and the unit having a methanation catalyst layer which performs a methanation reaction to reduce carbon monoxide contained in the concentrated hydrogen-containing gas, and a reaction temperature control section for controlling temperature of the catalyst layer at 250°C or more and 350°C or less, thereby selectively treating carbon monoxide. As the methanation catalyst, Ru carried by a carrier made of alumina may be used.