How Chronic Fatigue, Long Covid, and Fibromyalgia Affect Thyroid Health

Many people living with Chronic Fatigue Syndrome (CFS), Long Covid, or Fibromyalgia know the frustration of feeling exhausted, foggy, and unwell—often with no clear explanation from standard lab tests. One possible hidden factor? The thyroid gland.

The thyroid is a small gland in your neck that plays a huge role in how your body uses energy. It controls your metabolism, brain function, temperature, and more by producing hormones—mainly T3 and T4. If these hormones are off balance, even slightly, it can lead to symptoms that look and feel like chronic fatigue or fibromyalgia. But here’s the tricky part: many people in these groups show thyroid dysfunction that doesn’t show up on typical tests.

CFS and the Thyroid: A Hidden Link

People with Chronic Fatigue Syndrome (CFS) often report extreme exhaustion, brain fog, and trouble bouncing back from even mild physical activity. While doctors usually check thyroid hormone levels through a test called TSH, that test doesn’t always tell the full story.

In a 2018 study by researchers Ruiz-Núñez and colleagues, they looked more deeply at thyroid hormones in people with CFS. What they found was fascinating: many had normal TSH levels, but low levels of the active thyroid hormone T3, and high levels of something called reverse T3 (rT3)—a sort of "inactive" hormone that blocks the effects of T3. These patients also showed signs of inflammation and had low iodine levels, a nutrient crucial for thyroid function. So even though their tests looked “normal,” their cells were likely struggling to get the energy they needed (1)

Long Covid: Thyroid Disruption After Infection

Long Covid is another condition where the thyroid may be involved behind the scenes. After the initial COVID-19 infection, some people develop symptoms that linger for months: fatigue, foggy thinking, and body aches.

A 2025 review by Panesar and colleagues found that the virus responsible for Covid-19 can directly affect thyroid cells or trigger immune responses that disturb thyroid hormone production. One of the key culprits? Inflammatory molecules like IL-6, which can interfere with the brain's ability to control the thyroid, mess with hormone transport, and shift the balance away from active T3 toward inactive reverse T3. This pattern is known as non-thyroidal illness syndrome, and it’s your body’s way of conserving energy during stress or illness—but it can leave you feeling wiped out, even after the infection is long gone (2).

Another study even found that people who still couldn’t smell after Covid were more likely to have thyroid problems. It turns out the thyroid helps regulate nerve growth—including the nerves in your nose that handle smell. If the thyroid isn't working well, those nerves may not recover properly (3).

Fibromyalgia and the Thyroid: An Autoimmune Overlap

If you live with fibromyalgia, you know the struggle of chronic pain, fatigue, and sensitivity to pressure. What you might not know is that your immune system might also be targeting your thyroid.

In 2017, a group of researchers in Turkey found that a large number of people with fibromyalgia also had thyroid autoimmunity. That means their bodies were making antibodies that attack the thyroid gland—even if their hormone levels were still in the normal range. This silent attack may lead to thyroid damage over time or worsen symptoms like fatigue and brain fog (4).

Another more recent study in 2023 found that three out of four people with fibromyalgia tested positive for thyroid antibodies, and some even had low or high thyroid function, despite not knowing it (5).

A Common Thread: Stress, Hormones, and Inflammation

Although CFS, Long Covid, and fibromyalgia are distinct conditions, they share many of the same symptoms—and possibly the same underlying root: disruption of the brain-body hormone systems, especially the one connecting your stress response (HPA axis) and your thyroid gland.

When the body is under chronic stress or inflammation—as it often is in these conditions—it may produce more of the inactive hormone (reverse T3) and less of the active hormone (T3), even though the standard lab values look fine. This can leave people stuck in a state of “thyroid resistance”, where the body has the hormone, but can’t use it properly.

So What Can You Do?

If you have CFS, Long Covid, or fibromyalgia and suspect a thyroid issue, speak with your doctor about running more comprehensive tests (if available)—not just TSH, but also Free T3, reverse T3, and thyroid antibodies. In the UK, a comprehensive thyroid test is only available privately via a private GP or Registered Nutritional Therapist. Nutritional support and stress management may also help regulate this delicate system. Understanding the role of the thyroid in these conditions offers a valuable clue—and potentially a pathway to feeling better.