The article describes the case of a 60-year-old woman with long-standing COVID who had chronic fatigue and autonomic dysfunction more than 3 years after SARS-CoV-2 infection. Intestinal permeability (IP) was assessed at five time points by a carbohydrate absorption test. The results showed significantly increased lactulose/mannitol (L/M) ratios during episodes of worsening symptoms, including a second SARS-CoV-2 infection. Improvement in fatigue was correlated with reduction in IP. A probiotic regimen with Bacillus coagulans and Bacillus subtilis combined with medicinal clay resulted in further clinical improvement. This is the first report of IP assessment in a patient with long-term COVID with this test. The study highlights the correlation between changes in intestinal permeability and the severity of long-term COVID symptoms.