Background: Research suggests that psychological factors may influence vulnerability to SARS-CoV-2 infection, although the mechanisms are unclear. Purpose: We examined whether the hypothalamic-pituitary-adrenal axis may be a possible mechanism, by measuring the relationship between indices of psychological distress and cortisone in hair (hairE) in a UK cohort during the COVID-19 pandemic. Methods: Participants (N = 827) provided two 3 cm hair samples over a 6-month period between April-September 2020. Samples reflected hairE in the 3 months prior to the collection date. Results: HairE in the first samples (T1: commenced April 2020) did not differ significantly from pre-pandemic population norms. However, hairE in the second samples (T2: commenced July 2020) were significantly higher than T1 and pre-pandemic population norms, with a 23% increase between T1 and T2. Linear regressions, controlling for age and gender, demonstrated that at both timepoints, hairE levels were greatest in people with a history of mental health difficulties. In addition, stress reported at T1 predicted greater hairE at T2 and a greater change in hairE between T1 and T2. Conclusions: These findings demonstrate that during the COVID-19 pandemic hairE was substantially elevated across a large community cohort, with greatest levels in those with a history of mental health difficulties and greatest changes in those reporting greatest levels of stress early in the pandemic. Further research is required with verified SARS-CoV-2 outcomes to determine whether the HPA axis is among the mechanisms by which a history of mental health difficulties and stress influence SARS-CoV-2 outcomes.