Cases presenting with changes in various organs caused by anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination are rare. In particular, after such instances of vaccination, onset of subacute thyroiditis, Hashimoto thyroiditis, and Graves' disease was observed. We present the case of a 55-year-old woman whose hypothyroidism converted to hyperthyroidism after vaccination with Gam-COVID-Vac (Sputnik V). After the first dose of vaccine, a hormonal metabolism alteration was noted, i.e., conversion from hypothyroidism to euthyroidism. After the second dose of vaccine, onset of hyperthyroidism with thyrotoxicosis was noted without signs of subacute thyroiditis. Hyperthyroidism persisted for several weeks before reverting to hypothyroidism. Assessments did not reveal an increase in the patient's thyroid-stimulating hormone receptor antibody levels throughout the indicated period. However, after hyperthyroidism reverted to hypothyroidism, a significant increase in the peak systolic velocity of the superior thyroid arteries was observed, which is characteristic of hyperthyroidism. Owing to the known involvement of the autonomic nervous system (ANS) in blood vessel tone regulation, thyroid hormonogenesis, and stress, the ANS-mediated conversion from hypothyroidism to hyperthyroidism in certain individuals after receiving a vaccine, which may serve as a sufficient stimulus for ANS nerve centers, is highly probable. Therefore, diagnostic assessment of ANS condition should be performed before vaccination in patients with chronic thyroid disorders or diseases of other organs or organ systems. If changes in ANS are found, providing preemptive treatment before vaccination is recommended.