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.
