An apparatus and method of removing fixed pattern noise in a digital image processing apparatus are provided. The apparatus includes a controlling unit adjusting a number of image frames of a same image photographed by an imaging device and an exposure time of a shutter, and controlling a movement direction of the imaging device, which photographs the image; and a signal processing unit which median-combines the image frames of the same image photographed by the imaging device during the adjusted exposure time after moving the imaging device. The total photographing time is reduced by skipping a process of photographing a dark image and fixed pattern noise can be effectively removed by median-combining the image frames photographed while physically moving the imaging device between the photographing of consecutive image frames to remove the fixed pattern noise.