A growing number of findings indicate a relationship between COVID-19 infection and thyroid dysfunction. This association is also strengthened by knowledge on the potential of viral infections to trigger thyroid disorders, although the exact underlying pathogenetic process remains to be elucidated. This review aimed to describe the available data regarding the possible role of infectious agents, and in particular of SARS-CoV-2, in the development of thyroid disorders, summarizing the proposed mechanisms and levels of evidence (epidemiological, serological or direct presence of the viruses in the thyroid gland) by which the infection could be responsible for thyroid abnormalities/diseases. Novel data on the association and mechanisms involved between SARS-CoV-2 vaccines and thyroid diseases are also discussed. While demonstrating a clear causal link is challenging, numerous clues at molecular and cellular levels and the large amount of epidemiological data suggest the existence of this relationship. Further studies should be taken to further investigate the true nature and strength of this association, to help in planning future preventive and therapeutic strategies for more personal and targeted care with attention to the underlying causes of thyroid dysfunction.