Background:BK polyomavirus is one of the most common viral causes of late-stage hemorrhagic cystitis in pediatric allogeneic hematopoietic stem cell transplantation. However, there are no established diagnostic and therapeutic standards. This study examined the clinical features, risk factors, and treatment approaches of BK polyomavirus-associated hemorrhagic cystitis in pediatric hematopoietic stem cell transplantation patients. Methods:Pediatric patients who underwent hematopoietic stem cell transplantation at our center between January 2018 and October 2023 and developed BK polyomavirus-associated hemorrhagic cystitis were retrospectively included. Results:A total of 34 pediatric hematopoietic stem cell transplantation recipients with BK polyomavirus associated hemorrhagic cystitis were analyzed. Viruria was seen in all patients and viremia in 55.8% of patients. Hematuria was graded 1-4 in all patients; among which, 52.9% (18) had mild hemorrhagic cystitis (grades 1 and 2) and 47.1% (16) had severe hemorrhagic cystitis (grades 3 and 4). Bladder hematomas occurred far more frequently in severe hemorrhagic cystitis (p<0.01). Spontaneous recovery was more common in the mild hemorrhagic cystitis group (68.8%) than in the severe group (31.3%), whereas mortality occurred more frequently in severe hemorrhagic cystitis, although not BK polyomavirus-mediated (p=0.01). Treatment included immunosuppression reduction, intravesical and intravenous cidofovir, hyperbaric oxygen, and supportive care. Conclusions:BK polyomavirus associated hemorrhagic cystitis is a common and challenging complication in pediatric hematopoietic stem cell transplantation recipients. Clarification of risk factors and optimization of supportive and antiviral treatments can potentially reduce the morbidity of this process.