In a fluorescence tomography apparatus for obtaining fluorescence tomographic images of a region of an object to be observed: an application unit concurrently applies an ultrasonic wave and excitation light to the region so that ultrasound-modulated fluorescence is emitted from the region under the influence of the ultrasonic wave; and a first image acquisition unit acquires a fluorescence tomographic image of the region on the basis of the ultrasound-modulated fluorescence.