A method of manufacturing a silicon carbide semiconductor device includes the following steps. A silicon carbide substrate is prepared. A first mask layer is formed in contact with a first main surface of the silicon carbide substrate. The first mask layer includes a first layer disposed in contact with the first main surface, an etching stop layer disposed in contact with the first layer and made of a material different from that for the first layer, and a second layer disposed in contact with a surface of the etching stop layer opposite to the surface in contact with the first layer. A recess is formed in the first mask layer by etching the second layer and the etching stop layer. A first impurity region is formed in the silicon carbide substrate using the first mask layer with the recess. The first mask layer does not include a metallic element.