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Neck Pain at the Base of Skull

The pain at the base of the skull is unrelenting and getting worse.  It feels like a knife.  Physical therapy and medications have not helped.  Your appointment with your doctor is next month.  What are the major causes of neck pain at the base of the skull?  What are the treatment options for neck pain at the base of the skull?   Let’s dig in.


The base of the skull is a complex area.  It involves the upper cervical spine, facet joints, muscles, tendons, ligaments, and nerves.  Irritation or injury to any one of these structures can result in pain at the base of the skull.  Unfortunately, this area is not understood by many providers.  This can lead to a delay in treatment and unnecessary pain and suffering.

Causes of Neck Pain at Base of Skull

Muscle Tension/Strain

Near the base of the skull are a group of muscles called the suboccipital muscles. There are 4 paired muscles that attach to the upper two cervical bones (1).  The suboccipital muscles can become tense and tender due to factors such as eye strain, wearing new eyeglasses, poor ergonomics at a computer workstation, poor posture, and trauma.  This can result in neck pain at the base of the skull.

Facet Joint Injury

A facet is a small, cartilage-lined joint on the backside of the spine.  It is a paired joint with one on the right and one on the left at each level of the spine. For example, there is a right and left C2/3 and C3/4 facet joint and so on.  The facet joint guides and limits the motion of the spine.  The facets are susceptible to injury due to degeneration, trauma, surgery, and instability.  Facet injury can lead to persistent neck pain at the base of the skull (2).

Disc Injury

A disc is the shock absorber that is sandwiched between each spinal bone.  Like the facet joint, it is susceptible to injury due to degeneration, trauma, infection, surgery, and instability.  Disc injuries can cause inflammation, restricted movement, and neck pain at the base of the skull (3).

Ligament Injury

Ligaments are thick pieces of connective tissue that connect one bone to another.   There are a large number of ligaments that provide stability to the neck (4).  Examples include the supra and interspinous ligaments.  Ligaments can be injured through trauma such as a motor vehicle accident.  Ligaments can also be loose as a result of connective tissue disorders such as Ehlers-Danlos syndrome or hypermobility.  Damaged or loose ligaments can cause damage or irritation to the suboccipital muscles, facet joints, discs, and nerves.  Instability can cause multiple injuries and symptoms including base of neck pain.

Nerve Irritation

The greater, lesser, and third occipital nerves originate in the upper cervical area and travel to the base of the skull.  Unfortunately, they can be compressed by the neck muscles, ligaments, and fascia as they travel towards the base of the skull.  Compression of these nerves can cause a number of symptoms including headache and neck pain at the base of the skull.

Atlantoaxial Instability (AAI)

Instability simply means that bones move around too much, usually due to damaged ligaments. In the spine, this can cause nerves to get banged into and joints to get damaged. In the craniocervical junction, instability can cause the upper cervical spinal nerves to get irritated, leading to headaches. In addition, the C0-C1 and C1-C2 facet joints can also get damaged. In addition, there are other nerves that exit the skull here that can get irritated, like the vagus nerve, which can cause rapid heart rate. What’s the Difference Between CCI and AAI? CCI refers to instability in any part of the craniocervical junction…

Read More About Atlantoaxial Instability (AAI)

Cervical Medullary Syndrome

Cervical Medullary Syndrome is a clinical condition that occurs as a result of inflammation, deformity, or compression of the lower part of the brain. Symptoms can be extensive with fluctuating severity based upon the extent of the underlying injury. For example, mild irritation of the brainstem may cause only mild, intermittent symptoms. The upper cervical spine and brain are complex with multiple structures.  These structures reside within the skull and protective confines of the cervical spine.  Neither expands to accommodate inflammation, injury, and disease.  Rather the delicate tissues of the brain and spinal cord are irritated or compressed.   The 4 major conditions that cause cervical medullary syndrome are… 

Read More About Cervical Medullary Syndrome

Chiari Malformation

Chiari Malformation Is a medical condition where a part of the brain at the back of the skull abnormally descends through an opening in the skull. It is named after Dr. Hans Chiari who was an Austrian pathologist who in the late 1880’s studied deformities of the brain.The brain is a large structure divided into different parts that reside within the skull. Important parts of the brain called the Cerebellum and Brainstem sit at the base of the skull. The Foramen Magnum is a large hole at the base of the skull that allows the brain to join the spinal canal. The Cerebellum…

Read More About Chiari Malformation

Treatment Options for Neck Pain at Base of Skull

Treatment options depend upon the underlying cause of the pain.  Conservative therapy in the form of physical therapy when appropriate is the best first-line treatment.  Steroids are often recommended but should be avoided as they are toxic to orthopedic tissue and have significant side effects.  Nonsteroidal anti-inflammatory medications are also recommended but have significant risks.  Narcotics risk dependence.

At the Centeno-Schultz Clinic, we are experts in the evaluation and treatment of neck pain at the base of the skull.  Treatment options include PRP and bone marrow-derived stem cells. We pioneered the only nonsurgical treatment of upper cervical ligament injuries.  To learn more about ligament injuries in the neck and treatment options please click on the video below.

RELATED: How To Restore Natural Curve in Neck 

Consequences of Not Treating Neck Pain at Base of Skull

Treatment starts with having an accurate diagnosis.  Unfortunately during COVID in-person examinations are rare.  In-office examinations are brief at best with little or no physical examination. This is made worse by the fact the area is complex and not well understood by many providers.  The wrong diagnosis can lead to the wrong treatment which may ultimately lead to medication dependence, addiction, or life-altering surgery.

Consequences of No Treatment

  • Continued pain and suffering
  • Inability to enjoy family, friends, and favorite activities such as skiing, cycling, and walking
  • Possible dependence on NSAID or pain killers
  • Progression of the underlying muscle, facet, disc, or ligament injuries.  This in turn can limit treatment options.
  • Nerve injury which can become permanent.

In Conclusion

Neck pain at the base of the skull can be debilitating.  The 5 major causes of neck pain at the base of the skull are muscle strain, facet, disc, ligament, or nerve injury. Treatment options depend upon the underlying cause of the pain.  COIVD, telemedicine, and managed to care 5-minute evaluations have made it difficult to secure an accurate diagnosis.    Doctor google while informative can provide the wrong diagnosis.  If left untreated, the base of the skull can progress with increasing pain, suffering, isolation from family and friends, and injuries that can limit future treatment options.

If you or a loved one suffer from neck pain at the base of the skull please schedule telemedicine or in-person telephone candidacy with a physician at the Centeno-Schultz Clinic.  We are all board-certified, fellowship-trained with expertise in neck pain and regenerative options.  Stop the suffering and pain today


1.Yamauchi M, Yamamoto M, Kitamura K, et al. Morphological classification and comparison of suboccipital muscle fiber characteristics. Anat Cell Biol. 2017;50(4):247-254. doi:10.5115/acb.2017.50.4.247

2.Gellhorn AC, Katz JN, Suri P. Osteoarthritis of the spine: the facet joints. Nat Rev Rheumatol. 2013;9(4):216-224. doi:10.1038/nrrheum.2012.199

3.Peng B, DePalma MJ. Cervical disc degeneration and neck pain. J Pain Res. 2018;11:2853-2857. Published 2018 Nov 14. doi:10.2147/JPR.S180018

4.Leahy PD, Puttlitz CM. The effects of ligamentous injury in the human lower cervical spine. J Biomech. 2012;45(15):2668-2672. doi:10.1016/j.jbiomech.2012.08.012

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