The effect of noise light originating in a light guide portion is removed by simple calculations, and a clear fluorescence image that facilitates distinction between lesion tissue and normal tissue is acquired. Provided is a fluorescence endoscope apparatus including an insertion portion inserted into a body cavity; a light source unit that is disposed at a base end of the insertion portion and that emits excitation light and reference light that contains at least a part of the wavelength band of fluorescence produced by the excitation light; a light guide portion that guides the excitation light and the reference light emitted from the light source unit to a distal end of the insertion portion; an irradiation control unit that switches between a first irradiation state in which the excitation light guided by the light guide portion is radiated onto an inner wall of the body cavity and a second irradiation state in which the reference light is radiated onto the inner wall of the body cavity; an image-acquisition unit that acquires reflected light of the reference light and the fluorescence returning from the inner wall of the body cavity to the insertion portion; and an image computing unit that generates a fluorescence image signal by calculating the difference between a first image-acquisition signal acquired by the image-acquisition unit in the first irradiation state and a second image-acquisition signal acquired in the second irradiation state.