A stage control device including a position detection portion which detects a position deviation of a support plate relative to a reference position regulated by a convex portion provided in a stage, from an image of a scope including the support plate on which a sample is disposed and which is mounted on the stage; and a stage control portion that presses the stage, which is moved and controlled in a surface direction of the support plate so that the sample is in an imaging scope of an imaging element, from a position of a detection point in time in a direction corresponding to a position deviation at a pressing speed, and returns the stage up to a position of the detection point in time at a return speed slower than the pressing speed, when the position deviation of the support plate relative to the reference position is detected.