A method of manufacturing a silicon carbide semiconductor device includes ion-implanting an impurity in a surface of a silicon carbide wafer, and forming a carbon protection film of a predetermined thickness over all surfaces of the silicon carbide wafer, which has been ion-implanted with the impurity, by a chemical vapor deposition method that deposits a film by pyrolyzing a hydrocarbon gas. The method also includes annealing the silicon carbide wafer after the forming the carbon protection film.