Tension headaches, causing pain at the base of the neck, are the most common type of headache by a wide margin. The area between the upper cervical spine and the base of your skull is termed the sub-occipital region. This area is rich in nerve fibers, joints and small muscles -- all of which are capable of generating pain. Because this pain can indicate a life-threatening condition, see your doctor for an accurate diagnosis if you experience these symptoms.

Excessive Muscle Tension

Although not completely understood, tension headaches are assumed to be partly related to excessive muscle tension and contraction in the upper shoulders, neck, sub-occipital region and scalp. This tension is usually caused by sustained stress and poor posture, leading to inflammation and dull, achy pain. Tension headaches produce mild to moderate levels of diffuse pain distributed around the head in a band-like pattern that includes the back of the head and base of the neck.

Tension headaches may also result from changes among certain brain chemicals, such as serotonin and endorphins, which activate pain pathways and interfere with the brain's ability to suppress pain. In addition to stress and poor posture, jaw clenching, depression, dehydration and weak muscles could contribute to tension headaches and pain at the base of the neck.

Upper Neck Dysfunction

Cervicogenic headache pain is usually dull and localized near the base of the head, although it can become sharp with sudden neck movements, spreading up to the top of the head. Upper neck dysfunction can be caused by osteoarthritis, rheumatoid arthritis, apophyseal joint impingement or dislocation, nerve root irritation, and bulging intervertebral discs.cause:

• Upper neck dysfunction can be caused by osteoarthritis
  
• rheumatoid arthritis
  
• apophyseal joint impingement or dislocation
  
• nerve root irritation,
  
• bulging intervertebral discs

Disease Processes

Disease processes can cause headaches at the base of your neck. The Centers for Disease Control and Prevention notes that both bacterial and viral meningitis often start with a headache and a stiff neck, but usually also include fever, nausea and sensitivity to light 2.