Objective To investigate the factors affecting BK virus (BKV) clearance and analyze the effect of the course of viral clearance on graft function and long-term prognosis of renal transplant recipients with BK virus associated nephropathy (BKVAN). Methods Forty-nine cases of BKVAN confirmed by renal transplant biopsy, quantitative assay of urine cytology, and detection of DNA levels of BKV in urine and blood were selected. Patients underwent reduction of maintenance immunosuppression and the activity of BKV and renal function were monitored regularly. According to the clearance of BKV (including Decoy cell, viruria, and viremia), patients were divided into the clearance group and non-clearance group. Differences of serum creatinine between two groups and within group at diagnosis and 6 and 12 months after reduction of immunosuppression were compared. Differences of clinical indexes between two groups were also compared. The viral clearance time and 1-, 3-, and 5-year graft survival rates were calculated by Kaplan-Meier curves and the difference of graft survival rates between two groups were compared by Log-rank test. Results The clearance rates of Decoy cell, viruria, and viremia of recipients with BKVAN after reduction of maintenance immunosuppression were 63.8%, 27.7%, and 80.5%, respectively. The median clearance time of Decoy cell, viruria, and viremia calculated by Kaplan-Meier curves was 11, 41, and 5 months, respectively. Regular monitoring of BKV after surgery affected the viral clearance (P<0.05). The serum creatinine levels of the clearance group 6 and 12 months after reduction of immunosuppression were lower than or almost the same as those at diagnosis, while the serum creatinine levels of the non-clearance group 6 and 12 months after reduction of immunosuppression were higher than those at diagnosis. The difference of serum creatinine levels of the clearance group between 6 and 12 months after reduction of immunosuppression and at diagnosis were smaller than those of the non-clearance group (P<0.05). No acute rejection was observed after reduction of immunosuppression. The 1-, 3-, and 5-year graft survival rates of patients with BKVAN were 100%, 83.4%, and 66.4%. The 1-, 3-, and 5-year graft survival rates of the clearance group were significantly higher than those of the non-clearance group (P<0.05). Conclusion Regular monitoring of BKV after surgery and detection of BKVAN by early renal transplant biopsy is helpful for the clearance of BKV, which can affect the function and long-term survival rate of grafts.