Influenza virus infection is an important cause of mortality after hematopoietic stem cell transplantation (HSCT). Although early diagnosis followed by standard therapy with oseltamivir is thought to prevent influenza complications in myeloablative bone marrow transplant recipients, the optimal duration of therapy in these patients has not yet been determined. We describe a case of influenza virus reactivation, after remission had been achieved with standard oseltamivir therapy, in a patient undergoing nonmyeloablative bone marrow transplantation (NMBMT). A rapid diagnostic test (RDT) for influenza virus detection was performed with the ESPLINE Influenza A&B-N kit, which is a rapid, readily available, and widely used approach enabling highly specific and sensitive detection, as well as monitoring, of influenza A and B viruses. However, our case shows that a very low viral load that is undetectable by this RDT can reactivate influenza during the early phase of NMBMT. Our case suggests that oseltamivir administration for influenza infection should be continued, at least until successful engraftment, to prevent virus reactivation. The patient must be frequently and carefully monitored even after the resolution of symptoms and the clearance of viruses from respiratory secretions. The decision to cease oseltamivir therapy safely can be assisted by negative results on reverse transcription polymerase chain reaction (RTPCR) analysis.