Therapy for BK virus-associated hemorrhagic cystitis (BKV-HC) is limited after hematopoietic stem cell transplantation (HSCT). We examined whether choreito, a formula from Japanese traditional Kampo medicine, is effective for treating BKV-HC. Among the children who underwent allogeneic HSCT between October 2006 and March 2014, 14 were diagnosed with BKV-HC (median, 36 days; range, 14–330 days) after HSCT, and six consecutive children received a pharmaceutical-grade medicine, choreito extract granules. The hematuria grade before treatment was significantly higher in the choreito group than in the nonchoreito group (P = 0.018). The duration from therapy to complete resolution was significantly shorter in the choreito group (median, 9 days; range, 4–17 days) than in the nonchoreito group (median, 17 days; range, 15–66 days; P = 0.037). In 11 children with macroscopic hematuria, the duration from treatment to resolution of macroscopic hematuria was significantly shorter in the choreito group than in the nonchoreito group (median, 2 days vs. 11 days; P = 0.0043). The BKV load in urine was significantly decreased a month after choreito administration. No adverse effects related to choreito administration were observed. Choreito may be a safe and considerably promising therapy for the hemostasis of BKV-HC after HSCT.