Headaches and How to Find Relief: The Functional Medicine Way

functional medicine headache treatment
Learn about functional medicine headache treatment, various headache types, and how to achieve lasting relief with complementary approaches.

Headaches – painful, annoying, and seem to come on at the worst times. They are so common that they’re the 6th leading cause of disability worldwide. While the cause of headaches can vary, treatment is often more universal and natural treatment options for headaches exist.

But first, knowing about the different types of headaches can be helpful so you can treat them effectively. 

Types of Headaches

Headaches can be either primary or secondary. Primary headaches are often caused by a variety of factors we will look at below, while secondary headaches are the result of something else, like medications or other medical conditions for example. Let’s look at each.

Primary Headaches

Primary headaches – which make up approximately 90% of headaches in the general public – include daily persistent headaches, tension headaches, cluster headaches, and migraines. 

They are often triggered by lifestyle factors or situations such as:

  • Alcohol, especially red wine
  • Certain foods, like processed meats that contain nitrates. This is considered a food-triggered headache.
  • Consuming or withdrawing from nicotine. This is considered a nicotine headache, and can come on after smoking or if withdrawing from nicotine.
  • Changes in sleep or lack of enough good quality sleep.
  • Poor posture.
  • Physical activity. Known as an exertion headache, they can include pain during or after exercise, lasting either a few minutes up to two days after exertion.
  • Skipped meals, known as a hunger headache. Hunger headaches feel like dull headaches that go away after eating.
  • Coughing, sneezing, blowing your nose, straining such as when having a bowel movement, or laughing or crying vigorously. A primary cough headache often subsides quickly after a coughing episode – within 30 minutes of onset. 

Secondary Headaches

Secondary headaches are usually the result of something else – such as medications or medical conditions like:

  • Infection (viral, bacterial, or fungal)
  • Trauma, such as from a head or neck injury
  • Brain tumor
  • Aneurysm
  • Dehydration
  • Sinus headaches
  • Caffeine withdraw or too much caffeine
  • Hangover
  • Menstrual headaches
  • Vascular headaches, caused by high blood pressure or disorders of blood vessels
  • Psychiatric disease or as a consequence of psychiatric medications

The Difference Between Primary and Secondary Headaches

The main difference between primary and secondary headaches is that primary headaches have no physical/anatomical cause. Secondary headaches, on the other hand, are the result of something else going on in the body, such as another condition causing tension or inflammation. 

How To Diagnosis Headaches

Getting to the root cause of a headache is key to diagnosis. Your provider will obtain a robust history of your symptoms and gather the information needed to make the correct diagnosis. Some important information they may gather includes:

  • Headache frequency, duration, severity, and location of symptoms
  • Aggravating and alleviating factors
  • Timing of onset of symptoms
  • Family history of headaches
  • Lifestyle factors, including diet, sleep, caffeine use, and stress levels
  • Other associated conditions, such as sleep disorders, anxiety, depression, or underlying medical conditions

Diagnosis may also involve seeing a neurologist and getting imaging done like a CT scan or MRI. Talk with your functional medicine provider to find out the best course of action for diagnosis.

Natural Headache Treatments

While headaches can be frustrating, there are natural treatment options for headaches that work. 


Since certain foods can cause headache symptoms, it makes sense that nutrition and diet change can also impact headaches. For many, avoiding certain trigger foods like caffeine, alcohol, fermented foods, cheese, or chocolate can be beneficial. Caffeine especially is a trigger for people – with either too much or too little causing symptoms. Some find a moderate amount – 100 to 150mg a day – can keep headache symptoms at bay. 

More specifically, the ketogenic diet has been studied for its ability to provide neuroprotection and suppress neuroinflammation in the brain, helping decrease the severity and frequency of headaches. This is due to the elevation of ketone bodies when following the ketogenic diet, which have been found to be beneficial in the prevention of migraines

While nutrition and dietary changes can be beneficial, some can lead to nutritional deficiencies if followed too strictly without a balanced approach. This is where dietary counseling and selecting the appropriate diet for you can be helpful. Working with a functional medicine provider can help you create a personalized plan that targets your headache symptoms while also making sure you’re getting all the nutrients you need from your diet. 


Did you know that not getting good quality sleep can contribute to headaches? Or that untreated sleep apnea can significantly impact headaches? 

Sleep is so important in maintaining our well-being – and it also helps prevent headache symptoms. Getting high-quality sleep should be a priority for anyone suffering from headaches. The best way to do this? Avoid screens for at least an hour before bed, go to bed and wake up at consistent times each day, and keep your room dark and cool. Learn more ways to improve your sleep here.

Yoga and Stress Management

Exercise can be beneficial not only for general wellness, but also headache relief. Yoga has been studied in relation to its benefit of headaches, with evidence suggesting it reduces  headache frequency, duration, and lessens the intensity of pain in tension-type headaches. While more research is needed for yoga’s effects on migraines vs other forms of headaches, preliminary evidence is strongly supportive of yoga and its effects on tension-headache relief. In addition to the physiological benefits of yoga, its focus on mindfulness and deep breathing can support stress management to improve headache symptoms.

Avoid Toxins

Exposure to a variety of toxins – like secondhand smoke, allergens, strong odors from chemicals and even perfumes – can trigger headaches. Limiting your exposure to these is key. An air purifier can be great for helping with these sensitivities. The best place for an air filter is in your bedroom, since that’s where you spend the majority of your time. A few brands we highly recommend are the IQAir, Austin Air, and Molekule filters. Learn more about environmental toxins and how to detox from them here.

Body work

Body work therapy, such as massage therapy, chiropractic care and acupuncture are also helpful in the prevention and treatment of headaches. One study found that massage therapy was effective in reducing the number of headaches weekly when used consistently. This may be due to trigger points causing tension and inflammation, leading to headaches. Chiropractic and acupuncture can also provide headache relief – especially when the headaches are caused by trigger points in the muscles. 

Correct Hormone Imbalances

Changes in hormone levels can be a significant cause of headaches. We see this especially in menopause, when sex hormones are rapidly changing. Hormonal imbalances of the adrenal or thyroid glands can also be a cause of headaches. Identifying and treating these imbalances can oftentimes provide significant relief for headache sufferers. Working with a functional medicine provider to identify and treat hormonal imbalances for headache relief is a great place to start.

Treat Nutrient Deficiencies 

A variety of nutrient deficiencies can impact headache frequency, severity, and duration of symptoms. 


Scientific literature suggests that magnesium deficiency correlates with mild to moderate tension headaches and migraines. While magnesium deficiency can occur from a variety of reasons, such as not taking in enough through food or oral supplements, or an increased loss through the gastrointestinal tract or through the kidneys, it can be relatively easy to treat. When taken orally, magnesium helps relieve headaches – enough so that guidelines recommend it as a headache treatment.  Magnesium comes in several forms and is recommended for oral supplementation because of its ability to impact absorption on the intracellular level. With minimal side effects, magnesium is a great treatment option for those who are looking for an alternative headache treatment option, as it’s well-tolerated and inexpensive.  A great general magnesium that works well for most is magnesium glycinate, however magnesium l-threonate can also be helpful for headaches as well. 

B Vitamins

Studies suggest B2, B6, B9, and B12 reduce both the severity and frequency of migraines. Here’s a great, well-rounded B-complex vitamin to help. Vitamin B2, also known as riboflavin can be particularly helpful and has been studied in headache and migraine protocols. 


Increasing omega-3 fatty acids help reduce inflammation in the body, regulate vascular tone, and support gut health – all of which are beneficial for migraines. This is a great, well-rounded omega-3 fatty acid supplement to start, with a balance of EPA and DHA for best absorption.

Vitamin D3

Because of its many beneficial functions in the body, such as decreasing inflammation, providing immune system support, and modulating cellular growth, vitamin D impacts a variety of health conditions. A decrease of vitamin D has been linked to pain, psychiatric, gastrointestinal, musculoskeletal, and other disorders – including headaches. 

Studies have found that most people with migraines have low vitamin D levels, although more research is needed to support the connection between vitamin D and other types of headaches. Vitamin D supplementation is encouraged, especially for those with deficiency, as it helps reduce frequency of migraines. 

CoEnzyme Q10

CoQ10 is an important antioxidant for cardiovascular health, as it can help lower blood pressure and improve heart failure, but it can also be helpful for migraines as well. 

Other Supplements That May Be Helpful


Several studies show the correlation between a healthy gut and neurological health – including headaches. It’s been suggested that a healthy gut microbiome can help prevent or treat neurological disorders such as migraines and even Parkinson’s Disease. This is where probiotics come into play. Try adding in a complete probiotic supplement like this one to support a healthy gut microbiome. 


Oftentimes, chronic migraine sufferers have low melatonin levels. Melatonin helps regulate sleep-wake cycles, with the highest levels of melatonin occurring at night. By supplementing with melatonin, chronic migraine sufferers can often improve their quality and duration of sleep. While additional research is needed, preliminary findings support that a high quality melatonin supplement can help migraine sufferers with symptom management and offers a complementary approach to migraine treatment.

Natural Anti-inflammatories

Natural substances like curcumin, ginger and Boswellia may also help with headaches since they can reduce pain and inflammation. 


Butterbur, feverfew, and valerian can also be effective, especially in combination with some of the above therapies. 

Medications For Headache Relief

Both over the counter and prescription medications can provide headache relief. Over the counter medications that can provide temporary headache relief include things like ibuprofen, Tylenol, and aspirin. 

Common prescription medications for more serious headaches include:

  • Triptans like imitrex and zomig
  • Gabapentin
  • Topiramate
  • Divalproex
  • Erenumab (aimovig)
  • Certain blood pressure medications like beta blockers or calcium channel blockers

Functional Medicine and Headaches

Headaches can be debilitating. If you’re struggling with ongoing headaches and unable to find relief, functional medicine may offer the help you need. By taking a well-rounded approach to your health history, symptoms, and treatment options, functional medicine provides scientifically sound treatment options that get to the root of your symptoms. 

At Arizona Wellness Medicine, we treat your health as multi-functional, so we can understand your headache symptoms – helping you achieve lasting relief. Discover how our experienced functional medicine providers at Arizona Wellness Medicine can help with your headache symptoms here. 


  1. Headaches and Magnesium: Mechanisms, Bioavailability, Therapeutic Efficacy and Potential, Advantage of Magnesium Pidolate
  2. Headache
  3. What Can I Do to Avoid Headache and Migraine Triggers?
  4. Nicotine Headache
  5. Exertion Headaches
  6. Hunger Headache
  7. Primary Cough Headache
  8. Yoga for Treating Headaches: A Systematic Review and Meta-analysis
  9. Migraine and Diet
  10. The Role of Vitamin D in Primary Headache–from Potential Mechanism to Treatment
  11. The Pathogenetic Role of Melatonin in Migraine and Its Theoretical Implications for Pharmacotherapy: A Brief Overview of the Research
  12. B vitamins and their combination could reduce migraine headaches: A randomized double-blind controlled trial



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