Haemorrhagic cystitis (HC) is characterized by focal or diffuse haemorrhagic and inflammatory changes of the bladder mucosa. Polyoma BK virus (BKV) infection is an important underlying condition that provokes hematopoietic stem cell transplantation (HSCT)-related HC. Although commonly reported in transplant recipients, BKV associated HC, and tubulointerstitial nephritis rarely occurs in paediatric acute lymphoblastic leukemia (ALL) patients receiving chemotherapy. A 15-year-old girl diagnosed with T cell ALL, receiving high-risk chemotherapy protocol, complained about dysuria and lower abdominal pain with macroscopic haematuria. Her complaints started under meropenem, teicoplanin, amikacin, and caspofungin treatment due to neutropenic fever with severe mucositis. There wasn't any bacterial growth in the urine or blood culture. PCR analysis detected 2,2 × 109 copies/mL of BKV in urine. The antibiotics other than ciprofloxacin were discontinued. Her complaints are alleviated day by day. She did not experience any urinary symptoms or haematuria, and the BKV copy number declined to 3,3 × 107 copies/mL during follow-up.Contributing factors of BKV associated HC are highly relevant in HSCT recipients. However, patients receiving intensive chemotherapy may have similar conditions. A predisposing and potential manageable factor such as BKV should be searched in paediatric haematology practice.