The focused ion beam apparatus includes: an electron beam column; a focused ion beam column; a sample stage; a coordinate acquisition unit configured to acquire, when a plurality of irradiation positions to which the focused ion beam is to be applied are designated on a sample, plane coordinates of each of the irradiation positions; a movement amount calculation unit configured to calculate, based on the plane coordinates, a movement amount by which the sample stage is to be moved to a eucentric height so that the eucentric height matches an intersection position at which the electron beam and the focused ion beam match each other at each of the irradiation positions; and a sample stage movement control unit configured to move, based on the movement amount, the sample stage to the eucentric height at each of the irradiation positions.