The optimal management of hemorrhagic cystitis (HC) in hematopoietic stem cell transplantation (HCT) is debated, both for early onset HC (EOHC) secondary to chemotherapy toxicity and BK PolyomaVirus (BKPyV)-related HC, due to the lack of controlled trials, particularly referred to pediatric setting. Actually, clinical practice is mainly based on guidelines of European Conference on Infections in Leukemia, 6th edition, which consider both adult and pediatric population but conclude that, despite much progress in understanding the pathogenesis, epidemiology and risk factors, this complication still represents a disabling unmet clinical need with limited prophylactic and therapeutic options. Additionally, guidelines of American Society of Clinical Oncology define the management of chemotherapeutic toxicity independently from the patients’ population. A panel of experts belonging to the Hematopoietic Cell Transplant and Infectious Disease Working Group (WG) of Associazione Italiana di Emato-Oncologia Pediatrica (AIEOP) developed a consensus to define the best practices in prevention, diagnosis, and management of HC in pediatric HCT setting.