Provided is a fluorescence endoscope system for observing fluorescence from a fluorochrome attached to or absorbed in biological tissue, including an excitation light source that emits excitation light that excites the fluorochrome; an image-acquisition section that acquires fluorescence emitted from the biological tissue when irradiated with the excitation light from the excitation light source; an autofluorescence signal setting section that sets an autofluorescence signal intensity to be emitted from the biological tissue when irradiated with the excitation light; and an image compensation section that compensates fluorescence image information acquired by the image-acquisition section on the basis of the autofluorescence signal intensity set by the autofluorescence signal setting section.