An image analysis apparatus including a processor configured to: acquire a first fluorescence image indicating an observation target including a plurality of types of cells, each of which has a first region stained by first staining, and a second fluorescence image indicating the observation target in which a second region of a specific cell among the plurality of types of cells is stained by second staining different from the first staining; determine whether or not the first region is included in the second region in a superimposed image obtained by superimposing the first fluorescence image and the second fluorescence image and acquire a first determination result for each of the first regions; and determine the type of cell included in the observation target on the basis of the first determination result.