Provided is an endoscope system and a pixel correction method that are able to surely correct a blinking defective pixel in an image sensor. An endoscope system 1 includes: an illumination controller 33 that turns off a light source unit 31 in a predetermined cycle a difference calculation unit 52 that calculates difference data between a dark image corresponding to image data output from an image sensor 244 during lights-out time when the illumination controller 33 turns off the light source unit 31 and a dark reference image preliminarily generated to detect a blinking defective pixel in which the electric signal irregularly changes a blinking defective pixel detection unit 53 that detects a blinking defective pixel in the image sensor 244 based on the difference data calculated by the difference calculation unit 52 and a pixel correction unit 561 that corrects the electric signal output from the blinking defective pixel detected by the blinking defective pixel detection unit 53, by using electric signals output from neighboring pixels of the blinking defective pixel.
