An endoscope system includes an endoscope that acquires an image of a subject and a processor. The processor acquires position and posture information of the endoscope, estimates a three-dimensional shape of the subject based on the image and the position and posture information, generates, based on the position information, a cross section crossing a trajectory on which the endoscope passed, and determines an erroneous estimation portion based on a shape characteristic of the three-dimensional shape on the cross section.