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Abstract Objective and Background BK virus‐associated hemorrhagic cystitis (BKV‐HC) is an intractable complication leading to higher mortality and prolonged hospitalization among allogeneic hematopoietic stem cell transplantation (allo‐HCT) recipients. Therefore, identifying the potential risk factors of BKV‐HC after allo‐HCT is crucial to improve prognosis and for early prevention. However, the risk factors for BKV‐HC remain debatable. Therefore, we conducted a systematic review and meta‐analysis to identify the risk factors for BKV‐HC, for early prevention of the occurrence of BKV‐HC and to improve the quality of life and prognosis of allo‐HCT recipients. Methods We searched relevant studies from PubMed, EMBASE, and the Cochrane Library up to February 2023. The odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) of all risk factors were calculated to evaluate their effects on the occurrence of BKV‐HC. Results Overall, 11 studies involving 2556 allo‐HCT recipients were included in this meta‐analysis. All included studies were retrospective and published between 2013 and 2022. We found that male sex (OR = 1.32; 95% CI, 1.07–1.62; p  = .009, I 2  = 34%), haploidentical donor (OR = 1.84; 95% CI, 1.18–2.87; p  = .007, I 2  = 23%), myeloablative conditioning (OR = 1.76; 95% CI, 1.36–2.28; p  < .0001, I 2  = 45%), acute graft versus host disease (aGVHD) (OR = 2.73; 95% CI, 2.02–3.69; p  < .0001, I 2  = 46%), chronic graft versus host disease (cGVHD) (OR = 1.71; 95% CI, 1.12–2.60; p  = .01, I 2  = 0%), and cytomegalovirus (CMV) reactivation (OR = 3.13; 95% CI, 1.12–8.78; p  = .03, I 2  = 79%) were significantly associated with BKV‐HC in the univariable analysis. Conclusions Our meta‐analysis indicated that male sex, haploidentical donor, myeloablative conditioning, aGVHD, cGVHD, and CMV reactivation were potential risk factors for BKV‐HC.