There is provided a reformer for a fuel cell system, the reformer comprising: a reforming unit having a reaction substrate in which a catalyst layer is formed in a plurality of flow channels for allowing fuel to flow and for generating hydrogen through a reformation reaction of the fuel using thermal energy. When viewing a cross-section perpendicular to the flow direction of the flow channels, the reaction substrate defines each flow channel by a bottom portion and a pair of wall portions extending from the sides of the bottom portion, and a joint between the bottom portion and the wall portion is formed in a rounded shape. There is also provided a method of manufacturing a reaction substrate used for a reformer for a fuel cell system, the method comprising: (a) preparing a substrate; (b) anisotropically etching the upper surface of the substrate and forming a channel pattern of which a bottom portion and a wall portion are perpendicular to each other; (c) isotropically etching the channel pattern and forming a flow channel of which the joints between the bottom portion and the wall portions are rounded; (d) forming a support layer on the surface of the flow channel; and (e) forming a catalyst layer on the support layer.