A Functional Medicine Approach to Chronic Fatigue Syndrome: Understanding the Root Cause

Chronic fatigue syndrome (CFS) is one of the most common reasons people seek medical care, yet traditional treatments often fall short. Many individuals feel dismissed or unheard after being diagnosed, with limited options for true recovery. Functional medicine, however, offers a root-cause approach, addressing the underlying drivers of CFS rather than just managing symptoms.

Dr. Zimmerman at Peak Brain and Body in Wesley Chapel is a leading expert in helping individuals find answers and solutions for chronic fatigue syndrome through a non-pharmaceutical approach. His patient-centered approach focuses on identifying triggers such as infections, gut health, neurological dysfunction, and lifestyle factors.

In this article, we’ll explore what actually causes chronic fatigue syndrome, why traditional medicine struggles to treat it effectively, and how a chronic fatigue syndrome holistic treatment plan in functional medicine can lead to better outcomes.

If you prefer a video version: Watch It Here

Audio version: Listen Now

Understanding Chronic Fatigue Syndrome in Tampa

What Is Chronic Fatigue Syndrome?

Chronic fatigue syndrome, also known as myalgic encephalomyelitis (ME/CFS), is a complex condition characterized by extreme fatigue that doesn’t improve with rest. It is classified as a syndrome, meaning it consists of a set of correlated medical signs and symptoms rather than a specific disease with one defined cause.

There are a variety of symptoms individuals may experience: fatigue, weakness, dizziness, lightheadedness, nausea, brain fog, headache, tachycardia, allergies, and frequently getting sick. A proper chronic fatigue syndrome test may include immune system evaluation, blood sugar analysis, neurological exams, and gut health assessments to determine contributing factors.

Chronic fatigue syndrome is more common in females than males and is typically diagnosed when symptoms persist for six months or longer after ruling out other conditions like iron deficiency, blood sugar imbalances, thyroid dysfunction, or diabetes as the sole cause. With that being said, these can co-exist and may play a role in chronic fatigue syndrome.

The Overlapping Conditions of Chronic Fatigue Syndrome

One of the key challenges in treating CFS is its overlap with other conditions. Postural orthostatic tachycardia syndrome specialists often point out that POTS has significant symptom similarities, including dizziness, fatigue, brain fog, and immune dysfunction. Research shows that 95% of CFS patients experience worsening symptoms when moving from a seated or lying position to standing.

Rather than viewing CFS as a single disease, it’s more helpful to see it as a multi-system dysfunction impacting neurological, immune, gastrointestinal, musculoskeletal, and cardiovascular systems. This is why individuals are sent to a variety of specialists, but also struggle to get better.

What Causes Chronic Fatigue Syndrome?

The functional medicine approach to chronic fatigue syndrome starts with a fundamental question: What is driving the condition? Several contributing factors can set off the cycle of chronic fatigue, including infections, neurological dysfunction disorders, gut health issues, and immune dysregulation.

1. Pathogens and Chronic Infections Role in Chronic Fatigue Syndrome

Pathogens—including viruses, bacteria, fungi, and parasites—can play a significant role in the development and persistence of chronic fatigue. Some of the most common infectious triggers include:

• Epstein-Barr virus (EBV) – Often associated with reactivation in CFS patients. Note that most of the population has been exposed to EBV. The labs that would suggest an ongoing EBV issue include EBV early antigen IgG and EBV viral capsid antigen IgM.
• SARS-CoV-2 (Long COVID) – Can lead to post-viral fatigue and brain inflammation. Numerous studies have shown that the immune response can create a brain injury which explains why so many struggle with neurological symptoms after COVID.
• Herpes viruses – Including cytomegalovirus (CMV) and HHV-6.
• Lyme disease and co-infections – Bartonella, Babesia, and Mycoplasma pneumonia.
• Mold and mycotoxins – Often overlooked but significant in chronic fatigue cases.

Often, chronic infections and toxin exposure weaken the immune system, creating persistent fatigue. In some cases, mycotoxin testing is recommended to uncover mold exposure that may otherwise go undetected.

2. Neurological Dysfunction and Brain Inflammation

Chronic fatigue syndrome is often associated with neurological impairments, such as brain fog, dizziness, headaches, concentration, and word-finding difficulties. Research shows that inflammation in the body can cross the blood-brain barrier, triggering an immune response in the brain’s microglial cells. This leads to:

• Cognitive dysfunction (memory issues, poor concentration).
• Mood imbalances (anxiety, depression, irritability).
• Dysautonomia (heart rate and blood pressure irregularities).

Targeted therapies, such as functional neurology and neurological exercises, can help improve brain connectivity and restore energy regulation.

3. Gut Health and Chronic Fatigue Syndrome

The gut plays a crucial role in immune function and inflammation. Many CFS patients have dysbiosis (an imbalance of gut bacteria), which contributes to:

• Leaky gut (intestinal permeability) – Allowing inflammatory molecules to enter circulation.
• Low butyrate production – Reducing the gut’s ability to regulate inflammation.
• Inflammation spilling into the brain – Worsening cognitive symptoms and fatigue.

Addressing gut health through targeted nutrition, prebiotics, and probiotics can help improve overall energy levels and immune function.

Why Traditional Medicine Fails to Treat Chronic Fatigue Syndrome

In conventional medicine, treatment for CFS is typically symptom-based, often relying on stimulants or antidepressants for chronic fatigue syndrome. While these may provide temporary relief, they do not address underlying causes.

Symptom	Traditional Treatment	Functional Medicine Approach
Fatigue	Stimulants (Adderall, Modafinil)	Addressing infections, gut health, mitochondrial function
Brain Fog	Antidepressants, stimulants	Reducing neuroinflammation, improving brain connectivity
Pain	NSAIDs, muscle relaxants	Reducing systemic inflammation, targeted neurological exercises
Gut Issues	Laxatives, antidiarrheals	Restoring gut microbiome balance, healing leaky gut

Functional medicine, on the other hand, identifies and treats the drivers of CFS—whether they are pathogens, gut imbalances, brain inflammation, or environmental toxins. This difference explains why many patients feel more supported through a patient-centered approach in functional medicine.

A Functional Medicine Approach to Chronic Fatigue Syndrome in Wesley Chapel

Functional medicine goes beyond symptom management by performing in-depth testing to find the underlying factors driving the symptoms that make up this syndrome. We are going to explore some that that providers will often use when utilizing a functinal medicine approach to chronic fatigue syndrome. With this testing the provider is able to create personalized treatment plans. Here’s how it differs from conventional care:

1. Comprehensive Testing

A functional medicine provider will assess multiple body systems using tests such as:

• Advanced stool testing – Identifies gut imbalances and infections.
• Blood panels: to evaluate endocrine, metabolic, and vascular factors.
• Mold and mycotoxin testing – Evaluates mold exposure’s impact on the immune system. There is a dispute on the best testing: urine vs blood. We utilize blood testing that measures the immune response to mycotoxins and believe it is superior to urine. Having mycotoxins in urine doesn’t mean it’s creating an issue for the individual.
• Immune function panels – Measures inflammatory markers and immune imbalances.
• Neurological testing – Includes video oculography to assess brain function. We will discuss this more below as over 95% of functional medicine providers do not measure brain health and function.

Based on results, treatment is focused on restoring balance and supporting natural healing. This might include gut repair, detoxification, brain connectivity therapies, mitochondrial support, and neurological exercises.

2. Targeted, Root-Cause Treatments For Chronic Fatigue Syndrome

Once underlying causes are identified, treatment focuses on restoring balance. This may include:

• Mitochondrial support – Improving energy production with key nutrients like CoQ10, acetyl-L-carnitine, and B vitamins; but this is always done in conjunction with nutrition changes.
• Brain connectivity therapy – Strengthening brain function through functional neurology techniques.
• Gut repair protocols – Using dietary interventions and microbiome support. 
• Detoxification support – Removing toxins that contribute to inflammation by avoiding exposure and using targeted nutrition to support detoxification pathways in the body.
• Neuroinflammation reduction – Utilizing lifestyle strategies to calm the brain’s immune response.

3. A Holistic, Patient-Centered Approach

Unlike traditional medicine, functional medicine providers take the time to listen, analyze the full history, and develop an individualized plan. Lifestyle changes such as nutrition, sleep optimization, movement, and stress reduction play a central role in recovery.

The Missing Link: Functional Neurology

While functional medicine addresses many underlying causes of chronic fatigue syndrome, brain connectivity remains an overlooked factor. Functional neurology bridges this gap by:

• Evaluating eye movements to detect neurological dysfunction by using videooculography.
• Using balance testing to assess brain-body communication through computerized balance posturography.
• Providing targeted exercises to restore brain function and energy regulation.

In our experience, when these test results are off you can take all the supplements in the world but it’s not going to yield great results. The brain uses 25% of the entire body’s energy supply and to get someone out of a state of chronic fatigue by ignoring brain dysfunction is very hard. 

For the best results, working with a provider who combines functional medicine and functional neurology can provide a more complete approach to healing.

Final Thoughts

Chronic fatigue syndrome is a complex, multi-system condition that requires more than symptom suppression. A chronic fatigue syndrome holistic treatment through functional medicine provides long-term results by addressing root causes: chronic infections, leaky gut, neurological dysfunction disorders, pathogens, and blood sugar imbalances.

If you’re struggling with fatigue and conventional care hasn’t helped, our team at Peak Brain and Body offers a patient-centered approach that looks at the bigger picture.

Contact Dr. Zimmerman for Functional Medicine in Wesley Chapel and take the first step toward recovery today.

Ready to Take the Next Step?

If you’re looking for real answers to your chronic fatigue, reach out for a functional medicine consultation to start your path toward recovery today!

 

Do you suspect or know you have low thyroid? Or wondering, can a low thyroid cause headaches? Living with a low functioning thyroid can be a very difficult thing to deal with. Not only may you feel completely wiped out all the time, but you also might be noticing that it’s starting to affect your brain with symptoms such as brain fog, fatigue, fb-depression-lp, and even problems finding words.

If you don’t have to imagine these scenarios, because it is your daily life then you may have a low thyroid.

• Fall asleep at 10 pm and get up at 8 am hoping that sleeping 10 hours will give you the energy to chase your little one around at the park?
• Find yourself trying the latest diet fad hoping to shed a few pounds but it seems no matter how little you eat and how much you try to workout at the gym the scale just doesn’t ever seem to budge?
• You have to keep your hands in your pockets and wear two pairs of socks as it always feels like the tips of your fingers and toes are ice cold.
• You feel that your hair is starting to come out in clumps everytime you take a shower and if it continues you likely won’t have any hair left in a few months.
• You are at work in a meeting and you feel everything around you is happening so fast as it seems your brain is running in slow motion.

If you said yes to any of these, especially more than one. It is likely you may be suffering from a low thyroid, which is called hypothyroidism.

---

WHAT IS HYPOTHYROIDISM?

Hypothyroidism is when your thyroid isn’t producing enough thyroid hormones into the bloodstream. The thyroid gland’s main function is to control the rate at which each cell in the body functions by releasing two hormones: T4 and T3. The pituitary gland, which is part of your brain releases TSH which tells the thyroid gland to produce the hormones. T3 is the main hormone our body uses while T4 has to be converted to T3 within our gut and liver.

Because the thyroid hormones influence the rate at which every cell in the body functions it can cause symptoms with nearly every organ from your gut, liver, skin, and brain.

Common symptoms of hypothyroidism:

• Fatigue
• Weight gain
• Depression
• Brain Fog
• Headaches
• Hair Loss
• Dizziness
• Cold fingers and toes
• Constipation
• Problems with memory formation and finding words

Have you gone to your computer to complete a task only to find yourself staring blankly at the computer screen, unsure where to start as it seems you all of a sudden forgot why you went there to begin with?

Maybe you’ve had the experience of trying to do simple math, and you’re surprised at how your brain seems to trip over basic addition that you could previously rattle off in your sleep?

These are examples of brain fog, which is a common symptom of a low functioning thyroid.

Hypothyroidism can greatly affect the function of the brain by causing memory loss, mental fatigue, dizziness and headaches.

As if those symptoms aren’t bad enough, you have likely felt you are merely existing and noticing less motivation instead of the previous enjoyment you received on a daily basis.

Depression is just another symptom to the many that occur with hypothyroidism.

As you can see, an underactive thyroid can lead to a variety of symptoms. But can a low thyroid cause headaches?

---

HOW CAN A LOW THYROID CAUSE HEADACHES?

If you’ve noticed an increase in headaches, your thyroid function could be a contributing factor. Can a low thyroid cause headaches? Yes—it’s well documented that people with hypothyroidism are more likely to experience tension headaches and even migraines. When the thyroid isn’t producing enough hormones, blood flow can decrease, leading to reduced oxygen levels in the brain. This, combined with inflammation and hormonal imbalances, can result in persistent headaches.

Additionally, hypothyroidism can lead to brain fog, dizziness, and fatigue, all of which can intensify the frequency and severity of headaches. If you have been struggling with unexplained headaches alongside other symptoms like sluggishness, memory issues, or cold extremities, it may be worth investigating your thyroid function.

It’s important to ask, can a low thyroid cause headaches that worsen over time? The answer is yes, especially if thyroid function remains unaddressed. When left untreated, the impact on circulation and neurotransmitter balance can make headaches more frequent and severe.

---

A DEEPER LOOK INTO THYROID FUNCTION

So let’s say you relate to all or most of the examples given, but when you had your thyroid tested by your doctor, your tests came back normal and are told nothing is wrong. You start to doubt yourself and wonder if maybe you really are just depressed and that is causing everything else.

But you know something isn’t right and you’re tired of feeling fatigued all the time and the mental fog is starting to seriously affect your job and relationships – you just want answers and relief.

Here’s the thing, just because your tests came back normal, that doesn’t mean that you’re not experiencing the impacts of a low functioning thyroid. Unfortunately, there’s a deficiency in current testing where thyroid function isn’t looked at in a more detailed or deeper way.

For example, in school medical providers are taught to perform two main markers: TSH and T4. TSH is what tells the thyroid to produce T4. If TSH is elevated with T4 going low then you’d be diagnosed with hypothyroidism, but if that didn’t occur you’d be told nothing is wrong. T4 isn’t even the form the body uses the most, it is actually T3 which isn’t routinely evaluated..

The problem is that there are more values that can be obtained which provides much more insight, especially those which show an autoimmune response. Autoimmunity is when your body is attacking itself and it is responsible for 50-90% of all low thyroid cases.

With autoimmunity the type of thyroid you take can actually be making you feel worse and it isn’t as simple as getting your labs to be considered normal.

As you can see only running 2 lab markers can lead you astray. And here’s another thing, it’s possible that you’re experiencing symptoms of a low functioning thyroid not because of the thyroid itself, but because of an imbalance in the brain.

Remember, the brain is what tells the thyroid to produce hormones. If the brain is unhealthy and not able to properly communicate to the thyroid, then the thyroid will not produce the hormones appropriately. By taking a deeper look at the function of the brain and the pathways of communication, we can determine if your brain is affecting the release of thyroid hormones.

Imagine only having your thyroid labs evaluated without your brain being looked at, it will provide an incomplete picture. It should come as no surprise that a comprehensive evaluationshould be performed to best help you to identify what is causing your symptoms.

For these reasons nearly 30-50% of our patients who come in for thyroid concerns actually have no thyroid issues at all. For almost 25%, the thyroid is the main culprit of their symptoms.

---

HOW TO IMPROVE THYROID HEALTH

Luckily, there are things you can do to help improve thyroid health. Let’s take a look:

• Eating a healthy, balanced diet will provide your body with the nutrients to make thyroid hormones and promote a healthy gut..
• Limit the use of plastics and avoid using herbicides, pesticides, and commercial cleaning products to reduce your exposure to environmental toxins. Exposure to these toxins has a negative effect on hormones.
• Include iodine, selenium, and zinc in your diet. These trace elements improve thyroid function and can be found in seafood, walnuts, mushrooms, fish, and red meat. If you have autoimmunity you may need to be careful with iodine based products or food as it can make it worse.
• Exercise or have physical activity on a daily basis. We understand this may be the last thing you feel like doing, but losing excess weight helps to improve thyroid function.
• Take time for yourself and reduce stress. When your body is in a survival state this will impact your ability to produce thyroid hormones.

It’s essential to explore all factors when wondering, can a low thyroid cause headaches that persist despite medication? If your symptoms remain despite treatment, it could indicate an underlying imbalance that needs to be addressed.

HOW OUR BRAIN, MIND, & BODY METHOD CAN PROVIDE YOU WITH THE ANSWERS YOU SEEK

If you’re still reading, it is because you are looking for help and want answers.

• With our BMB method you can experience:
• Waking up feeling well-rested and excited for the day ahead.
• Move throughout your day with a clear mind, staying focused and confident in the tasks before you.
• Exercise without feeling completely weakened and drained.
• Able to fully listen and carry a conversation with a loved one. Listening will no longer feel strained and you won’t have to have the embarrassing moment of forgetting what you were going to say!
• Go on a walk with your friend or spouse after a workday because you finally have the energy to.

So how does our BMB method help you to get to the bottom of your symptoms and be able to live life again?

We start by evaluating you as a whole person as we understand how a dysfunction in one area can impact another. For this reason we start with a comprehensive evaluation with allows us to identify what is preventing you from living the life you want by:

• Evaluating brain function by studying brain waves, balance, and eye movements.
• Looking at the function of each body system by studying symptoms and lab results.
• Looking at past traumas, both physical and emotional, and how they may be affecting you today.

If you’re still asking, can a low thyroid cause headaches that interfere with daily life? then it’s time to take action. Request your free health strategy session today, and we will help you get the answers you need!