Provided are a processor device, an endoscope system, and a method of operating a processor device, which can narrow down an index value necessary for diagnosis of a lesion from among a plurality of index values. An image obtained by imaging an observation target including a structure is acquired. The index value calculation unit (70) performs an index value calculation process for calculating a plurality of index values obtained by indexing the properties of the structure based on the image. After the index value calculation processing unit (74) calculates the first index value among the plurality of index values, the index value calculation unit (70) is operated according to the processing order for calculating the second index value different from the first index value. Control.
