This case report describes a 22-year-old female patient who developed refractory grade IV BK virus-associated late-onset hemorrhagic cystitis on day 69 following haploidentical hematopoietic stem cell transplantation. Conventional stepwise interventions including bladder irrigation, repeated transcatheter arterial embolization, and endoscopic electrocoagulation failed to control the disease. On day 84 post-transplant, the patient received a combination of umbilical cord-derived mesenchymal stem cells and intravenous cidofovir. Following this combined therapy, bladder hemorrhage was progressively controlled, dysuria was relieved, and transfusion requirements decreased. Macroscopic hematuria began to decrease on day 98 post-transplant and resolved completely by day 124, accompanied by a marked decline in BK viral load. This case suggests that the combination of mesenchymal stem cells and cidofovir may serve as a potential salvage strategy for severe, refractory virus-associated hemorrhagic cystitis.