A training data generating system includes a processor. The processor acquires a plurality of medical images. The processor associates medical images with each other which are included in the plurality of medical images based on similarities of an imaging target to generate an associated image group including medical images associated with each other. The processor outputs, to a display, an application target image to be an image as an application target of representative training information based on the associated image group. The processor accepts input of representative contour information indicative of a contour of a specific region in the application target image as the representative training information. The processor applies contour information, as training information, to each medical image included in the associated image group based on the representative training information input to the application target image.