They are called cervicogenic headaches, meaning the headache did, indeed, start in the neck. Although headaches can arise from a variety of causes (stress, allergies, insomnia, accident, etc.) many do originate in the neck or from neck trauma.
The anatomy of the neck helps to explain the connection, because there are three nerves that exit the neck and travel to the head (C1, C2, and C3). The first, C1, the lesser occipital nerve, travels to the back of the head, so when it is irritated, the headache will present here. While the C2 nerve, the greater occipital nerve, travels to the back of the head and continues on to the top of the head, where it can communicate with the trigeminal nerve referring pain into the forehead or behind the eye. The last nerve, C3, is the greater auricular nerve, and it travels to the area just above the ear. The pain from an irritated nerve can present as pain, numbness, tingling, burning or even itching.
These cervicogenic headaches indicate that the sensations are coming from the neck, and thus, need to be treated at the neck level. Manipulation and adjustments improve pain and function and along with exercises to rehabilitate the muscles, reduce the time needed for recovery.
What about Migraines? These headaches are different and may be preceded by blurry vision, auras, tingling sensations, or even sensory dysfunction such as smells or tastes. While Migraines are often caused by allergies, over-stressed nervous systems, or inflammation, sufferers reported fewer attacks and less medication when combined with chiropractic care. But, very few are eliminated by manipulation.
Notwithstanding, spinal manipulation is very safe, and a trial is often helpful even if the headaches are only reduced because there are very few side effects.