Provided are a radiography system, a radiography method, a radiography program, and a body thickness estimation apparatus that can estimate the body thickness of a subject using each of radiographic images generated by irradiation with radiations having different energy levels.A radiography system includes a radiography apparatus including two radiation detectors and a console including an estimation unit that estimates the body thickness of a subject on the basis of the ratio of pixel values in a region, which corresponds to a soft tissue of the subject and is a corresponding region of radiographic images generated by the two radiation detectors irradiated with radiations having different energy levels, and correspondence relationship information in which the ratio and the body thickness are associated with each other.