Long COVID vs Chronic Fatigue: Are They the Same Thing? A Functional Medicine Perspective

Author: Rohan Smith | Functional Medicine Practitioner | Adelaide, SA

Quick Answer

Long COVID and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) are not formally the same diagnosis. However, current research suggests substantial biological overlap. Both are classified as post-viral syndromes and are commonly associated with persistent fatigue, post-exertional malaise, cognitive dysfunction, immune dysregulation, and chronic inflammation (1–4). From a functional medicine perspective, Long COVID may, in some individuals, activate or reflect similar underlying pathophysiological pathways observed in ME/CFS rather than representing an entirely distinct condition.

Core Concept: Post-Viral Syndromes Explained

Post-viral syndromes describe a group of conditions in which symptoms persist for months or years after an acute infection has resolved. Common triggering infections include influenza, Epstein–Barr virus (EBV), and SARS-CoV-2 (5,6). Instead of returning to physiological baseline, the body appears to remain in a prolonged state of immune or metabolic stress.

Both Long COVID and ME/CFS are increasingly understood as systemic conditions rather than isolated organ diseases. This systems-based understanding helps explain why standard investigations are often unrevealing despite significant functional impairment. For a broader overview of this pattern, see our guide on chronic fatigue.

Shared Biological Mechanisms

Mitochondrial Dysfunction

Mitochondria are responsible for cellular energy production. Research indicates that impaired mitochondrial function may be present in both ME/CFS and Long COVID, leading to reduced ATP generation and disproportionate fatigue following physical or cognitive exertion (7–9). This mechanism is closely linked to post-exertional malaise, a defining feature of ME/CFS.

Immune Dysregulation

In post-viral conditions, immune signalling may remain chronically activated or become functionally suppressed. Studies have identified altered cytokine profiles, impaired antiviral responses, and immune exhaustion in both Long COVID and ME/CFS populations (10–12). In some individuals, these changes are associated with autoantibody formation or reactivation of latent viruses such as Epstein–Barr virus.

Persistent Inflammation

Low-grade, chronic inflammation has been documented across both conditions. Neuroinflammation, in particular, is thought to contribute to cognitive symptoms such as impaired concentration, sensory sensitivity, and mood disturbance (13,14). Inflammatory signalling may also interfere with mitochondrial efficiency and autonomic nervous system regulation, including effects on the gut microbiome.

Why Conventional Testing Often Appears “Normal”

Standard medical investigations are designed to identify overt pathology rather than functional dysregulation. Routine blood tests may not capture subtle abnormalities in immune signalling, mitochondrial performance, autonomic balance, or inflammatory mediators (15).

As a result, individuals may be told that test results are normal despite ongoing symptoms. This reflects limitations in diagnostic sensitivity rather than an absence of physiological dysfunction.

How Functional Medicine Investigates Root Contributors

Functional medicine focuses on identifying underlying physiological contributors that may be perpetuating symptoms. Assessment is guided by detailed clinical history and may include:

• Immune and inflammatory markers to assess ongoing immune activation or viral reactivation
• Gut microbiome analysis to evaluate dysbiosis and immune–gut interactions
• Hormonal evaluation, including thyroid and adrenal signalling patterns
• Nutrient status testing relevant to energy production and cellular repair

Results are interpreted as interconnected patterns rather than isolated abnormalities, supporting a systems-level understanding of why recovery may be incomplete.

Will Long COVID Progress to ME/CFS?

Not everyone with Long COVID will meet diagnostic criteria for ME/CFS. However, longitudinal studies suggest that a subset of individuals with persistent post-COVID symptoms may later fulfil ME/CFS definitions, particularly when post-exertional malaise and significant functional limitation are present (16,17).

In other cases, Long COVID may reveal pre-existing vulnerabilities in immune, metabolic, or autonomic regulation rather than causing a new condition entirely.

When to Consider Further Investigation

Further assessment may be appropriate when symptoms persist beyond three months following infection, particularly if fatigue is disproportionate to activity, worsens after exertion, or is accompanied by cognitive, autonomic, or gastrointestinal symptoms.

Next Steps

A comprehensive, individualised evaluation may help clarify which biological systems are contributing to ongoing symptoms. This approach is intended to complement, not replace, conventional medical care by addressing functional contributors that standard testing may overlook.

Key Insights

• Long COVID and ME/CFS share significant biological overlap
• Post-exertional malaise is a key distinguishing feature
• Immune and mitochondrial dysfunction are central mechanisms
• Normal routine tests do not exclude meaningful physiological dysfunction

Ready to Explore Your Next Steps?

If persistent post-viral fatigue is affecting your quality of life, a functional medicine consultation may help identify contributing factors. A discovery call can clarify whether this investigative approach is appropriate for your situation.

References

1. NICE. Myalgic encephalomyelitis (or encephalopathy)/chronic fatigue syndrome: diagnosis and management. 2021.
2. World Health Organization. A clinical case definition of post COVID-19 condition. 2021.
3. Komaroff AL, Bateman L. Will COVID-19 lead to myalgic encephalomyelitis/chronic fatigue syndrome? Front Med. 2021.
4. Davis HE et al. Characterizing long COVID in an international cohort. EClinicalMedicine. 2021.
5. Hickie I et al. Post-infective and chronic fatigue syndromes precipitated by viral infections. BMJ. 2006.
6. White PD et al. Post-viral fatigue: epidemiology and pathophysiology. BMJ. 2001.
7. Myhill S, Booth NE, McLaren-Howard J. Chronic fatigue syndrome and mitochondrial dysfunction. Int J Clin Exp Med. 2009.
8. Tomas C et al. Cellular bioenergetics in chronic fatigue syndrome. PLoS One. 2017.
9. Appelman B et al. Mitochondrial metabolism in long COVID. Nat Metab. 2024.
10. Montoya JG et al. Cytokine signature associated with disease severity in ME/CFS. PNAS. 2017.
11. Phetsouphanh C et al. Immunological dysfunction in long COVID. Nat Immunol. 2022.
12. Su Y et al. Multiple early factors anticipate post-acute COVID-19 sequelae. Cell. 2022.
13. Nakatomi Y et al. Neuroinflammation in ME/CFS. J Nucl Med. 2014.
14. Albrecht DS et al. Brain glial activation in post-viral fatigue. Brain Behav Immun. 2019.
15. Naviaux RK. Metabolic features of the cell danger response. Mitochondrion. 2014.
16. Jason LA et al. A longitudinal analysis of ME/CFS diagnostic criteria following infection. J Transl Med. 2021.
17. Twomey R et al. Post-exertional symptom exacerbation in long COVID. JAMA Netw Open. 2022.