Most of the time the causes of anal pain are benign, even if there is bleeding. The pain is experienced during a bowel movement but may persist over time. You may also . What to Expect From a Prolapsed Hemorrhoid. Find out about common and less common causes of anal pain (pain in the bottom ), a burning or gnawing pain that lasts several hours after doing a poo; rectal An anal fistula is a small tunnel that develops between the end of the bowel. You'll know you have an anal fissure if you experience pain during or after your bowel movements (poop passing by an open wound = serious.