A method of manufacturing a semiconductor device includes: forming, on or above a GaN-based semiconductor layer, an electron beam resist containing chlorine; forming, in the electron beam resist, a first opening that exposes a portion of a surface of the semiconductor layer; forming a film of a shrink agent that covers a sidewall surface of the first opening; and forming, in a state in which the sidewall surface is covered by the film of the shrink agent, a Ni film that contacts the semiconductor layer through the first opening.