Provided are an image processing device, a radiography system, an image processing program, and an image processing method which can generate a tomographic image used for radiographic interpretation and a tomographic image suitable for generating a composite two-dimensional image from a projection image obtained by tomosynthesis imaging. A frequency processing unit and a tomographic image generation unit generate a first tomographic image which is emphasized according to a spatial frequency and is used for radiographic interpretation, on the basis of the projection images obtained by tomosynthesis imaging, and generate a second tomographic image which is emphasized according to the spatial frequency and on which the degree of emphasis is different from the degree of emphasis on the first tomographic image, on the basis of the projection image. A two-dimensional image generation unit combines a plurality of second tomographic images to generate a composite two-dimensional image.