In a method of manufacturing a mask blank adapted to be formed with a resist pattern by electron beam writing and having a light-shielding film and an etching mask film of an inorganic-based material resistant to etching of the light-shielding film which are formed in this order on a transparent substrate, when forming the etching mask film, shielding is performed using a shielding plate so as to prevent the etching mask film from being formed at least at a side surface of the substrate.