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The COVID-19 pandemic altered everyday life starting in March 2020. These alterations extended to the lives of children as their normal routines were disrupted by community lockdowns, online learning, limited in-person social contact, increased screen time, and reduced physical activity. Considerable research has investigated the physical health impact of COVID-19 infection, but far fewer studies have investigated the physiological impact of stressful pandemic-related changes to daily life, especially in children. The purpose of this study was to leverage an ongoing clinical trial to investigate physiological consequences associated with chronic stress of pandemic community lockdown on children. As a part of the clinical trial, children provided saliva samples. Saliva samples were analyzed for cortisol and salivary alpha amylase (sAA) content. This secondary cross-sectional analysis included 94 preadolescent children located within the Greater Boston, Massachusetts community. Children participated in the study either before, during, or following the pandemic community lockdown to form three groups for comparison. In response to chronic stress caused by the pandemic community lockdown, participants demonstrated dysregulation of fast-acting catecholamine response of the locus-coeruleus-norepinephrine system and slower-acting glucocorticoid response, resulting in an asymmetrical relationship of hypocortisolism (M = 0.78 ± 0.19 μg/mL, p < 0.001) paired with higher sAA (M = 12.73 ± 4.06 U/mL, p = 0.01). Results suggest that the abrupt COVID-19 disruption to daily life, including the stressful experience of community lockdown …