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Background: maladaptive changes in the autonomic nervous system (ANS) have been observed in short and long-term phases of COVID-19 infection. Identifying effective treatments to modulate autonomic imbalance could be a strategy for preventing and reducing disease severity and induced complications. Objective: to investigate the efficacy, safety, and feasibility of a single session of bihemispheric prefrontal tDCS on indicators of cardiac autonomic regulation and mood of COVID-19 inpatients. Methods: patients were randomized to receive a single 30-min session of bihemispheric active tDCS over the dorsolateral prefrontal cortex (2 mA; n = 20) or sham (n = 20). Changes in time [post-pre intervention] in heart rate variability (HRV), mood, heart rate, respiratory rate, and oxygen saturation were compared between groups. Additionally, clinical worsening indicators and the occurrence of falls and skin injuries were evaluated. The Brunoni Adverse Effects Questionary was employed after the intervention. Results: there was a large effect size (Hedges’ g = 0.7) of intervention on HRV frequency parameters, suggesting alterations in cardiac autonomic regulation. An increment in oxygen saturation was observed in the active group but not in the sham after the intervention (P = 0.045). There were no group differences regarding mood, incidence and intensity of adverse effects, no occurrence of skin lesions, falls, or clinical worsening. Conclusions: a single prefrontal tDCS session is safe and feasible to modulate indicators of cardiac autonomic regulation in acute COVID-19 inpatients. Further research comprising a thorough assessment of autonomic function and inflammatory biomarkers is required to verify its potential to manage autonomic dysfunctions, mitigate inflammatory responses and enhance clinical outcomes.