In accordance with an embodiment, a pattern inspection apparatus includes a stage supporting a substrate with a pattern, a light source irradiating the substrate with light, a detection unit, an optical system, a focus position change unit, a control unit, and a determination unit. The detection unit detects reflected light from the substrate. The optical system leads the light from the light source to the substrate and leads the reflected light to the detection unit. The focus position change unit changes a focus position of the light to the substrate in a direction vertical to the surface of the substrate. The control unit associates the movement of the stage with the light irradiation and controls the stage drive unit and the focus position change unit, thereby changing the focus position. The determination unit determines presence/absence of a defect of the pattern based on the signal from the determination unit.