Introduction: Reactivation of cytomegalovirus (CMV) infection is a major threat and it causes significant morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). There remains, however, a paucity of evidence regarding the economic burden of current CMV management in Japan. The aim of this study is to characterize the healthcare resource utilization (HCRU) and cost incurred for CMV management post allo-HSCT, using a Japanese hospital claims database. Methods: Patients who underwent allo-HSCT between April 2010 and March 2018 were identified and followed up for 180 days. Results: In total, 916 patients were included for analysis and categorized into CMV (À) group and CMV (þ) group based on the presence of a CMV episode within 100 days post allo-HSCT. A CMV episode was defined as evidence of receiving at least one dose of the following anti-CMV drugs, ganciclovir, foscarnet, or valganciclovir. The mean (± standard deviation [SD]) total length of stay was 93.6 (± 43.7) days in the CMV (þ) group, which was significantly longer than 55.9 (±40.6) days in the CMV (À) group, and this trend was more pronounced in patients with multiple CMV episodes. The mean (±SD) total medical cost within 180 days post allo-HSCT was US$122,328 (±56,977) in the CMV (þ) group, while the mean total medical cost was US$75,344 (±43,821) in the CMV (À) group. Moreover, transfusion and antimicrobial use was observed as the major medication cost component, which is suggestive of the indirect effect of CMV episodes. Conclusion: This study demonstrated that CMV episodes post allo-HSCT were associated with increased HCRU and cost.