If muscles are more used to working in fits and spurts they are more likely to burn sugars without using oxygen. This is called anaerobic metabolism , and it doesn't work nearly as well as aerobic metabolism. As the muscles use up the nutrients and oxygen, they switch to anaerobic metabolism and chemical waste products are created that can cause pain in the muscles. Aerobic training increases the muscles ability to get rid of these waste products. Exercise has other benefits as well.
Exercise can cause chemicals called endorphins to be released into the blood.
These chemical hormones act as natural pain relievers in reducing your pain.