Autoimmune pancytopenia (AIP) is known to be caused by coexisting autoantibodies against three lineages of blood cells. We report a rare case of autoimmune pancytopenia (AIP) which was preceded by refractory anemia. An 85-year-old man with a 4 and half-year history of unexplained anemia presented in October 2016 because of remarkable pancytopenia and fever. Since direct and indirect anti-globulin tests as well as anti-platelet antibody were positive, Evans' syndrome was initially suspected. However, the patient also had remarkable neutropenia. Additional examination for anti-neutrophil antibody showed the presence of anti-neutrophil IgG antibody specific for human neutrophil alloantigen (HNA)-1a and HNA-2. A diagnosis of AIP was thus established. Subsequent steroid therapy was effective for improving thrombocytopenia as well as neutropenia; nevertheless, the improvement of anemia seemed insufficient. Furthermore, a transient thrombocytopenia appeared 2 months after admission during the treatment. This event in addition to a febrile episode and elevated levels of CRP, β2-microglobulin and soluble interleukin-2 receptors seen at initial presentation prompted us to investigate if there had been specific infections by using the previously stocked serum samples. Consequently, the patient was found to have cytomegalovirus (CMV) infection; the presence of CMV-IgM antibody as well as CMV-DNA was demonstrated in the serum at the reappearance of thrombocytopenia. Since positive CMV-IgG and negative CMV-IgM were retrospectively confirmed in the stocked serum at initial presentation, it was considered that a reactivation of CMV occurred during the hospital course. The bone marrow aspirations carried out during hospitalization were compatible with refractory anemia, indicating that the patient already had refractory anemia before developing AIP.The recognition of AIP should be a requisite for the correct diagnosis in some cases of Evans' syndrome associated with leukocytopenia. Special consideration should be given to the possible involvement of CMV infection in pathogenesis of autoimmune cytopenia(s) or AIP. Insufficient recovery from anemia seemed to be related with coexisting refractory anemia.