A substrate processing apparatus which irradiates a substrate under processing with an electron beam and processes the substrate with the electron beam is disclosed. The substrate processing apparatus includes an electron beam generation mechanism which generates the electron beam, first area having a plurality of first static electricity deflecting devices whose thicknesses gradually increase in a traveling direction of the electron beam, and a second area disposed on a downstream side of the electron beam of the first area and having a plurality of second static electricity deflecting devices whose thicknesses are nearly same in the traveling direction of the electron beam. The substrate processing apparatus may further include a plurality of lenses whose thicknesses gradually decrease in the traveling direction of the electron beam, at least one of the plurality of lenses being disposed in each of the first area and the second area.