Exercise is beneficial for many health conditions, but Long COVID is different. For people with post-exertional malaise (PEM), pushing through symptoms can trigger significant deterioration rather than improvement. This article explains why, what current research shows, and how pacing differs from graded exercise therapy.
You went to your GP. You explained that you cannot do what you used to do. That you crash after basic activities. That you feel worse after trying to push through. And you were told, with genuine kindness and absolutely no malice, to exercise more. Maybe gently. Maybe with a referral to physio. Maybe with the reassuring addition of “your body just needs to get moving again.”
You went home, tried it, and spent the next week in bed.
And now you are reading this because you want to understand what happened, and maybe also because you want something you can politely but firmly hand to the next clinician who suggests a brisk walk will sort things out.
This article is that thing.
Perhaps you’ve been told to “just build your fitness back up.” You tried. You went for a short walk, attended a rehabilitation class or followed an exercise programme because you genuinely wanted to recover. Then, instead of getting stronger, you spent the next few days barely able to get out of bed. If that sounds familiar, you’re not alone and current research helps explain why.
Why does the “just exercise” advice exist at all?
It is not coming from nowhere. For most conditions involving fatigue and reduced activity, exercise genuinely is one of the best interventions available. Chronic fatigue following hospitalisation, general deconditioning, depression, cardiac rehabilitation: exercise works. The evidence base is solid and well established.
The logic applied to Long COVID patients goes roughly like this. You have been ill. You have been less active. Being less active leads to deconditioning. Deconditioning makes fatigue worse. Therefore: exercise to reverse the deconditioning. It is internally coherent. The problem is that for a significant proportion of Long COVID patients, the premise is wrong.
The thing you actually have is not deconditioning. It is post exertional malaise, and those are not the same condition.
What post exertional malaise actually is
Post exertional malaise (PEM) is a hallmark feature of Long COVID and ME/CFS. It is not simply feeling tired after activity, in the way a healthy person might feel tired after a long run. It is a pathological, delayed, disproportionate worsening of symptoms following physical, cognitive or emotional effort that can take 12 to 48 hours to fully arrive and can last days or weeks.
You walk to the kitchen, feel fine, and then wake up the next morning feeling like you got hit by a bus. That is not deconditioning. That is PEM. And the solution to PEM is not more walking.
Why is PEM so often misunderstood?
One reason is timing. Most illnesses make you feel worse during the activity itself. PEM often waits until hours later or even the following day. By then, neither the patient nor the clinician always connects the crash with the activity that triggered it. This delayed response is one reason people are repeatedly told they are simply “out of shape,” when in reality their body is responding abnormally to exertion.
Why exercise makes things worse: the muscle biopsy study
Here is where the science gets genuinely alarming, and also where the “just exercise” advice moves from unhelpful to potentially harmful.
In January 2024, researchers at Vrije University Amsterdam published a study in Nature Communications that took muscle biopsies from Long COVID patients before and after exercise. What they found was not deconditioning. They found mitochondrial dysfunction, severe muscle damage, a disturbed immune response, and a buildup of microclots in muscle tissue that all worsened after exercise. One of the study’s authors described it as a very real disease visible at basically every parameter measured, as reported in this NPR article on the Nature Communications muscle biopsy findings.
To spell that out: exercise is not rebuilding the muscles of Long COVID patients with PEM. It is actively damaging them further. The mitochondria, which are the energy producing structures inside every cell, show measurably worse function after exercise in these patients, not better.
A separate MR spectroscopy study published in 2024, measuring mitochondrial function in the gastrocnemius muscle during and after exercise, found that Long COVID patients had significantly impaired phosphocreatine recovery rates compared with healthy controls, as documented in this MR spectroscopy study on mitochondrial dysfunction in Long COVID. The muscle is not recovering between efforts the way a deconditioned but otherwise healthy muscle would. Something is genuinely broken at the cellular level.
A 2024 study in the Journal of Translational Medicine also confirmed that on the second day of a two day exercise test, ME/CFS and Long COVID patients showed a significant decrease in peak oxygen consumption and reached their anaerobic threshold at a much lower workload. This is documented in this overview of GET controversy and ME/CFS evidence. In a healthy person, a second day of exercise testing produces similar results to the first. In these patients, the second day is measurably worse. That is not deconditioning. That is a body that cannot recover normally from exertion.
The PACE trial, graded exercise therapy, and the slow institutional reckoning
The “exercise more” paradigm for post viral fatigue has deep institutional roots. It was built largely on a cognitive behavioural model that held fatigue in these conditions was perpetuated by unhelpful beliefs and avoidance behaviour. If the patient believed they were ill and avoided activity, they became deconditioned, which made them more ill. The treatment, therefore, was to gradually increase activity while addressing the psychological barriers to doing so.
This model underpinned the PACE trial, a large UK study of graded exercise therapy (GET) and cognitive behavioural therapy (CBT) for ME/CFS, which was published in The Lancet in 2011 and became enormously influential. It was also extremely controversial. Critics, including many of the researchers now working on Long COVID, raised serious concerns about the methodology, the outcome measures, and the framing of recovery in the study.
The British NICE guidelines, updated in October 2021 after an extensive evidence review, concluded that graded exercise therapy is harmful and should not be used, and that cognitive behavioural therapy is only an adjunctive and not a curative treatment. This is covered in this PMC paper analysing the PACE trial GET manual. The CDC in the United States removed GET from its ME/CFS recommendations. Major health authorities around the world began revising their guidance.
The problem is that these institutional shifts take time to reach every GP, every physiotherapy referral pathway, and every hospital rehabilitation service. In the meantime, patients who came through the door with Long COVID were being sent to services designed around a model that had already been formally rejected for conditions that Long COVID closely resembles.
The clinical trial problem: most Long COVID exercise studies do not even measure PEM
Here is something that should make everyone considerably more frustrated. Of 112 exercise related trial registrations for Long COVID, only 21 mentioned PEM at all. Only 14 actually assessed it, with two specifically excluding participants with moderate to severe PEM, and two others excluding any participants with PEM whatsoever. This is documented in this Sick Times analysis of PEM in Long COVID exercise trials.
You cannot study whether exercise is safe for patients with PEM if you remove all the patients with PEM from your study and then do not measure PEM in the ones who are left. The exercise trial evidence for Long COVID is therefore, at its core, evidence about Long COVID patients who either do not have PEM or have mild enough PEM to be enrolled. That evidence is then routinely applied to patients whose entire presenting problem is severe PEM. This is a gap so large you could drive a hospital bed through it.
So when is exercise actually appropriate in Long COVID?
Here is the nuance that matters, because this is not an article arguing that Long COVID patients should never move.
The key distinction is PEM. Its presence changes everything.
For Long COVID patients with POTS or dysautonomia and without significant PEM, specific, very carefully structured movement can be appropriate and may genuinely help. The emphasis here is on recumbent or aquatic exercise that avoids orthostatic stress, meaning no upright cycling or treadmill walking in the early stages, because standing up in POTS is already a cardiovascular event without adding exercise on top of it. The Open Medicine Foundation clinical care guide specifies recumbent exercises such as rowing, swimming, recumbent cycling, Pilates and yoga for POTS, and only when PEM is not induced, as stated in this OMF clinical care guide for Long COVID and ME/CFS.
For Long COVID patients with PEM, the evidence supported approach is not graduated increases in activity. It is pacing, which means staying within your energy envelope and not crossing the threshold that triggers a crash. The energy envelope is different for every person and can be very small. Some people in severe states are managing in units of minutes per day, not hours. Pushing against the boundary of this envelope does not expand it. It shrinks it.
The practical question is always: do your symptoms reliably worsen 12 to 48 hours after exertion? If yes, that is PEM, and any exercise advice that does not account for this is advice designed for a different patient.
What to do with a clinician who still recommends graded exercise
You are allowed to push back. You can do this politely and with evidence.
You can mention the 2021 NICE guidance that explicitly removed GET from recommendations for ME/CFS and similar post viral presentations. You can mention the Vrije University muscle biopsy study in Nature Communications. You can ask whether the exercise programme being recommended has been assessed for safety in patients with post exertional malaise. You can ask for a referral to a Long COVID clinic or a clinician familiar with ME/CFS rather than a generic physiotherapy service.
You are not refusing to engage with your recovery. You are asking for your recovery to be managed according to the evidence that currently exists, not the evidence from a model that was already retired before you became ill.
Key Takeaways
- Exercise is not universally harmful in Long COVID.
- The presence of PEM changes the approach completely.
- Research shows biological abnormalities after exertion in people with PEM.
- Pacing aims to prevent crashes, not avoid activity forever.
- Rehabilitation should be individualised rather than one-size-fits-all.
Frequently asked questions
Why do doctors still tell Long COVID patients to exercise more?
Because the standard treatment paradigm for fatigue and deconditioning involves graduated activity increases, and many clinicians have not yet updated their practice to reflect what the research on PEM in Long COVID and ME/CFS now shows. It is not malice. It is an evidence gap that is closing too slowly.
What is the difference between deconditioning and post exertional malaise?
Deconditioning means the body has become less fit due to reduced activity, and responds normally to graded reintroduction of movement. Post exertional malaise means the body responds to exertion with a pathological, delayed worsening of symptoms that exercise makes worse, not better. They require opposite approaches.
Is graded exercise therapy harmful in Long COVID?
For patients with PEM, the evidence strongly suggests it is. The 2021 NICE guidelines removed GET from ME/CFS recommendations after an extensive evidence review. Muscle biopsy research in Long COVID patients shows that exercise worsens mitochondrial dysfunction and causes measurable muscle damage.
What does the muscle biopsy research actually show?
A 2024 Nature Communications study found that Long COVID patients with PEM show worsening mitochondrial function, more severe muscle damage, immune infiltration and microclot accumulation in muscle tissue after exercise, not the rebuilding and adaptation seen in healthy people or deconditioned but otherwise well patients.
Can exercise help POTS in Long COVID?
In patients with POTS who do not have significant PEM, specific recumbent or aquatic exercise avoiding orthostatic stress may be appropriate and helpful. This is very different from general aerobic exercise, walking programmes or upright cycling. It must be carefully monitored and paced.
What is pacing and how is it different from GET?
Pacing means identifying your energy limits and staying within them to avoid triggering PEM crashes. GET means incrementally increasing activity regardless of symptoms on the premise that the body will adapt. These are opposite approaches. Pacing has evidence of being safe in ME/CFS and Long COVID. GET has evidence of being harmful.
How do I know if I have PEM?
If your symptoms reliably worsen in the 12 to 48 hours after physical, cognitive or emotional effort, and that worsening lasts more than a day, this pattern is consistent with PEM. It is worth specifically naming this pattern to your clinician rather than simply describing fatigue.
What should I do if my physiotherapist is recommending a graded exercise programme?
Ask specifically whether the programme has been assessed for safety in patients with post exertional malaise, and whether the therapist is familiar with the NICE 2021 guidelines on ME/CFS and similar post viral conditions. If not, ask for a referral to a Long COVID clinic or a practitioner with specific experience in PEM.
Why do exercise studies in Long COVID show conflicting results?
Because most of them do not measure or exclude for PEM. Studies showing benefit from exercise are often studying patients who do not have significant PEM. Applying those results to patients who do is like testing a drug in one population and assuming it works the same way in a completely different one.
Will I always have to avoid exercise?
For most people, no. As Long COVID stabilises and PEM becomes less severe, many people gradually find more activity is tolerable. The goal of pacing is not permanent inactivity. It is protecting the nervous system and energy systems from crashes that can push recovery backwards, so that genuine improvement over time is possible.
This article is for general information and education. It does not replace personalised medical advice. If you are uncertain about exercise and your specific Long COVID presentation, please speak with a clinician familiar with post exertional malaise.
Sources and further reading
Muscle biopsy and mitochondrial research Muscle abnormalities worsen after post exertional malaise in Long COVID, Nature Communications 2024: https://www.nature.com/articles/s41467-023-44432-3 MR spectroscopy assessing mitochondrial dysfunction in Long COVID, Radiology 2024: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694076/Long COVID mitochondrial damage and exercise, NPR: https://www.npr.org/sections/health-shots/2024/01/09/1223077307/long-covid-exercise-post-exertional-malaise-mitochondria Day 2 CPET findings and anaerobic threshold in ME/CFS and Long COVID: https://www.rthm.com/resources/blogs/graded-exercise-controversy-me-cfs
Guidelines and policy NICE guideline analysis and GET PACE trial review, Life 2025: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12028393/ CBT and GET in ME/CFS and Long COVID, Frontiers in Human Neuroscience 2025: https://pmc.ncbi.nlm.nih.gov/articles/PMC11814198/ Pacing versus GET systematic review, ScienceDirect 2025: https://www.sciencedirect.com/science/article/pii/S1360859225002025
The PEM gap in trial design Less than 20% of Long COVID exercise trials mention PEM, The Sick Times November 2025: https://thesicktimes.org/2025/11/21/less-than-20-of-long-covid-trials-involving-exercise-even-mention-post-exertional-malaise/ No evidence supports using GET for ME/CFS, Medscape October 2025: https://www.medscape.com/viewarticle/no-evidence-supports-using-graded-exercise-myalgic-2025a1000tuf
POTS and appropriate movement Practical recommendations for exercise in Long COVID with and without PEM, PMC 2024: https://pmc.ncbi.nlm.nih.gov/articles/PMC11043268/ OMF clinical care guide for Long COVID and ME/CFS, Bateman Horne Center 2025: https://batemanhornecenter.org/wp-content/uploads/2025/05/Clinical-Care-Guide-First-Edition-2025.pdf
Last reviewed and updated: July 2026.
This article reflects current research on post-exertional malaise, mitochondrial dysfunction, exercise physiology and Long COVID rehabilitation. It includes evidence from peer-reviewed studies together with international clinical guidance. As understanding of Long COVID continues to evolve, this article will be reviewed and updated to incorporate important new evidence.