Acquired amegakaryocytic thrombocytopenia (AAT), a rare entity characterized by severe thrombocytopenia and the absence of megakaryocytes in the bone marrow, may mimic or precede the diagnosis of aplastic anemia (AA). Here, we describe a patient who presented with apparent Epstein-Barr virus (EBV)-associated immune thrombocytopenia resistant to several lines of therapies, which was in fact a form of AAT with some features of AA. He eventually responded to therapy with eltrombopag, cyclosporine A (CSA), and antithymocyte globulin (ATG) and recovered completely. EBV infection is known to cause a variety of benign and malignant hematologic disorders, including bone marrow failure. However, to the best of our knowledge, this is the first case report of EBV-associated AAT. Treatment options for AAT are still not well defined, and even response to eltrombopag together with CSA and ATG does not always imply successful therapy. The natural history of EBV infection may well be sufficient to explain unexpected eventual recovery.