An endoscope apparatus includes a processor including hardware. The processor is configured to implement an image acquisition process that acquires a plurality of in vivo images; an in-focus evaluation value calculation process that calculates an in-focus evaluation value that represents a degree of in-focus corresponding to each of the plurality of in vivo images; a focus control process that controls a focus operation of an imaging optics by performing a control process that switches a position of a focus adjustment lens included in the imaging optics between a plurality of discrete positions based on the in-focus evaluation value; and a freeze image setting process that selects at least one in vivo image from the plurality of in vivo images based on the degree of in-focus represented by the in-focus evaluation value, and sets the selected at least one in vivo image to be a freeze image.