A method for manufacturing a semiconductor device having a MOS transistor, includes forming a gate electrode material layer on a first insulating film formed on a semiconductor substrate, forming an etching mask on the gate electrode material layer, forming a gate electrode by patterning the gate electrode material layer such that a protective film that protects at least a lower portion of a side face of the gate electrode and a portion of the first insulating film, which is adjacent to the side face, is formed while the gate electrode material layer is patterned, forming a second insulating film on the semiconductor substrate on which the gate electrode is formed, and forming an interlayer insulation film on the second insulating film.