An endoscope system that appropriately reduces time for alignment as needed when, for example, emphasizing a tissue of interest or the like by using a plurality of images obtained by imaging an observation target at different timings to achieve both the frame rate and the accuracy of, for example, emphasizing the tissue of interest or the like, a processor device, and a method for operating the endoscope system are provided. The endoscope system includes an image acquiring unit that acquires a first image and a second image, the first image being obtained by imaging an observation target by using first illumination light, the second image being obtained by imaging the observation target by using second illumination light that is different from the first illumination light at a different timing from the first image； an alignment unit that aligns the first image and the second image； and an accuracy changing unit that changes an accuracy of the alignment in accordance with at least a structure of interest to which an attention is paid in the observation target.
