Objective To investigate the gene expression of breast cancer resistance protein (BCRP) in bone marrow of acute leukemia (AL) and its prognosis. Methods A total of 67 AL patients admitted in our hospital from January 2014 to December 2014 were enrolled in the study, and 10 healthy volunteers were involved as control group. Real-time PCR was utilized to measure the gene expression of BCRP in bone marrow. And the difference in the BCRP gene expression and its prognosis were analyzed. Results The gene expression of BCRP in bone marrow of AL patients was statistically higher than that in the healthy volunteer group (P < 0.01). Acute leukemia patients were divided into high BCRP group and low BCRP group according to the mean of BCRP (3.0). Compared with low BCRP group, the primary WBC count was higher in BCRP high group (P < 0.01). The survival analysis between the two groups was statistically significant (Log-rank = 21.78, P < 0.05). Conclusion The gene expression of BCRP in bone marrow of AL patients was statistically increased and associated with the prognosis. High BCRP gene expression was a risk factor for poor prognosis in patients with AL.