Systemic fungal infection (SFI) is now one of the main causes of death from infective complications after hematopoietic stem cell transplantation (HSCT) and the role of prophylaxis of fungal infection has been established. However, there is no evidence evaluating the cost-benefit ratio of SFI management in Japan. To estimate the medical costs on prophylaxis and treatment of SFI in HSCT, we embarked on a randomized control prospective study of the medical cost-benefit ratio comparing fluconazole with itraconazole for antifungal prophylaxis in 40 patients who received HSCT in our hospital. Despite the similarity of efficacy for prophylaxis, the median cost of itraconazole prophylaxis between Day-10 and Day+28 was significantly less than that of fluconazole. There are many patients who require an i.v. formulation because of non-compliance with oral administration after HSCT and these cases cause increased medical costs. Therefore, further investigation is needed not only regarding differences among prophylactic agents but also regarding differences in administration routes focusing on the cost-effectiveness of treatment.