A pattern inspection method according to one aspect of the present invention includes generating a first positional deviation amount map by using data acquired by a pre-scan, generating a second positional deviation amount map by using data acquired by a full scan, generating a first positional deviation difference map by calculating a difference between the first positional deviation amount map and the second positional deviation amount map, generating a third positional deviation amount map from the first positional deviation difference map and the second positional deviation amount map, and judging existence of a value exceeding an allowable value, in values defined by the third positional deviation amount map.