Subacute thyroiditis is a rare disease in childhood and is considered postviral in origin. Epstein-Barr virus (EBV) involvement has been suspected, but just once demonstrated in an adult female. We report a case of subacute thyroiditis during infectious mononucleosis in a 3-year-old girl. The diagnosis of infectious mononucleosis was supported, in addition to the typical clinical symptoms, by presence of EBV DNA both in plasma and leukocytes. Subacute thyroiditis was diagnosed based on elevated thyroid hormone levels with thyrotropin (TSH) suppression, high inflammation markers and almost absent (99)TC uptake by thyroid. Moreover after 3 months from diagnosis thyroid function went back to normal as well as the (99)TC uptake.