The present technology relates to an endoscope system in which resolution and an S/N ratio are adjusted to be well-balanced depending on an imaging condition, and further capable of changing a processing load depending on the imaging condition, a method for operating the endoscope system, and a program.From an image signal in a body cavity imaged by an endoscope apparatus, a low frequency image including a low frequency component and a high frequency image including a high frequency component are extracted. The low frequency image is reduced by a predetermined reduction ratio, and, after image quality improvement processing is performed, is enlarged by an enlargement ratio corresponding to the reduction ratio. At that time, based on condition information indicating an imaging state, when brightness at the time of imaging is sufficient and the high frequency component does not include noise components a lot, the low frequency image and the high frequency image are added to be output as an output image. In addition, based on the condition information, when the brightness at the time of imaging is not sufficient and the high frequency component includes the noise components a lot, only the low frequency image is output as the output image. The present technology can be applied to the endoscope system.