Introduction: We present a case of Hashimoto's thyroiditis and severe autonomic dysfunction three months after the resolution of the acute phase of COVID-19 infection in a patient with no prior thyroid disease and autonomic dysfunction. Patient Review: We discuss our patient's clinical presentation, diagnostic evaluation, and subsequent management and follow-up. The patient had previously tested positive for COVID-19. A 53-year-old female developed Hashimoto's thyroiditis with normal thyroid function and severe autonomic dysfunction. Her heart rate variability (HRV) is depressed, and her High-Frequency power (HF) is high. Conclusion: Our findings suggest that COVID-19 could have long-term negative effects on antithyroid antibodies. Therefore, testing antithyroid antibodies should be included in the follow-up algorithm for COVID-19 survivors. Autonomic nervous system dysfunction related to COVID-19 may be reversible and early aggressive therapy is necessary. The new technique is important for the early detection of post-acute sequelae of SARS-CoV-2 infection (PASC) in the autonomic nervous system.