PROBLEM TO BE SOLVED: To provide a scanning-type confocal endoscope system and an image capturing method capable of easily and stably performing calibration without using a fluorescent paint.SOLUTION: A scanning-type confocal endoscope system comprises: a scanning-type confocal endoscope for irradiating a subject with excitation light and receiving fluorescent light excited by the excitation light a processor for generating a fluorescent image for normal observation on the basis of the fluorescent light received by the scanning-type confocal endoscope and an index for the calibration, wherein at calibration, the scanning-type confocal endoscope irradiates the index with light of a predetermined wavelength different from that of the fluorescent light, and receives the reflected light of the light of the predetermined wavelength, and the processor generates an image of the index on the basis of the reflected light of the light of the predetermined wavelength received by the scanning-type confocal endoscope.
