Yes, all pain is in the brain. The brain is the control center and pain is like a complicated alarm system that is set to protect you by telling you when something needs attention. Without pain we may not realize that there is a problem that needs attention. The brain’s job is to analyze all the information it receives from all of our senses and determine what kind of pain, how much pain, whether or not to give us pain.
The amount of pain we experience is unrelated to the severity of the injury. In certain situations such as an emergency or in a battlefield, pain is often not felt until after the emergency is over or the solder have made it to safety. On the other hand, some amputees feel pain in the limb that isn't there.
For example, in a situation where you touch something hot, a signal is sent you brain. Your brain instantly sounds off the alarm telling you that you feel pain and to take your hand away before too much damage is done. The initially physical pain is caused by tissue damage. In some situations, however, the pain remains long after the healing process is complete. The brain has made a decision regarding the tissue, and sometimes that decision doesn't make sense. It has concluded that creating pain will serve you and has changed the sensitivity level of what sets off the pain alarm.
In many cases of chronic back pain, the alarm system has become too sensitive. Some folks stop their activities once pain starts and only focus on dealing with their pain. Their brain’s alarm system becomes more and more sensitive and over time their lifestyle starts to shrink.
In these cases, dealing with chronic pain is frequently about resetting the alarm system to function normally again.