A method of manufacturing a silicon carbide semiconductor device includes a step of preparing a silicon carbide substrate having a first main surface and a second main surface located opposite to the first main surface, a step of forming a doped region in the silicon carbide substrate by doping the first main surface with an impurity, a step of forming a first protecting film on the doped region at the first main surface, and a step of activating the impurity included in the doped region by annealing with the first protecting film having been formed, the step of forming a first protecting film including a step of disposing a material which will form the first protecting film and in which the concentration of a metal element is less than or equal to 5 μg/kg on the first main surface.