Disclosed is a fluorescence image analyzing apparatus including a light source that emits light to a sample including a plurality of cells labeled with a fluorescent dye at a target site, an imaging unit that captures a fluorescence image of each of the cells that emit fluorescence by being irradiated with the light, a processing unit that processes the fluorescence image captured by the imaging unit, and a display unit that displays the fluorescence image processed by the processing unit. The processing unit performs an extraction process of extracting, for each cell, a plurality of bright spots in the fluorescence image including the target site, a changing process of changing a pixel value of each of the plurality of extracted bright spots based on the pixel value of each bright spot, and a display process of displaying the fluorescence image whose pixel value is changed on the display unit.