Headache pain generated from neck structures is often referred to as cervicogenic headache. Treatment may not be different but the area of concentration may change.
For example, the pain relievers or other medications used for headache pain probably won't be any different. But manual therapy approaches used by the physical therapist or chiropractor may be applied to the cervical spine (or other parts of the spine).
A home program of exercise and self-management that goes beyond rest and relaxation may be possible. Postural and muscle imbalances that might be part of the problem can be identified and corrected.
Your doctor or therapist will be able to apply what are referred to as best practice methods in treating cervicogenic headache pain. This means they can search the medical literature for guidelines on this topic.
Ask your doctor what his or her best recommendations are for you with this new diagnostic information. Don't give up if recovery doesn't occur right away. Chronic pain is a complex issue. Sometimes, even with a correct (or more accurate) diagnosis, the problem is not resolved immediately. Give yourself some time to try each step in this new approach.