An endoscope apparatus includes: a light source apparatus that emits light in a wavelength band including a first wavelength band for exciting a first fluorescent substance and a second wavelength band; an image pickup section that picks up an image of first fluorescence emitted when the first fluorescent substance is excited and an image of second fluorescence emitted when a second fluorescent substance provided on a treatment instrument is excited, to generate a fluorescence image; an information storing section that stores shape information including information on a shape of the second fluorescent substance; and an operation section that performs an operation to estimate an actual size of a region in which the first fluorescence is generated, based on a scaling factor calculated based on the shape information and a size of a draw region of the second fluorescence, and a size of a draw region of the first fluorescence.