A new type of coronavirus named as SARS-CoV-2 pandemic has begun to threaten human health. As with other types of coronaviruses, SARS-CoV-2 affects children less frequently, and it has been observed that the disease is mild. In the pathogenesis of a standard viral infection, the pathogen's contact with the mucosa is initially followed by an innate immunity response. T cells are the primary decisive element in adaptive immunity capability. For this reason, the adaptive immune response mediated by the thymus is a process that regulates the immune response responsible for preventing invasive damage from a virus. Regulatory T cells (T-reg) are active during the early periods of life and have precise roles in immunomodulation. The thymus is highly active in the intrauterine and neonatal period; it begins to shrink after birth and continues its activity until adolescence. The loss of T-reg function by age results in difficulty with the control of the immune response, increased inflammation as shown in coronavirus disease (COVID-19) as an inflammatory storm. Also, the thymus is typically able to replace the T cells destroyed by apoptosis caused by the virus. Thymus and T cells are the key factors of pathogenesis of SARS-CoV-2 in children.