Objective To explore the potential mechanisms of mesenchymal stem cell (MSC) therapy in ischemia/reperfusion injury (IRI)-induced acute kidney injury (AKI). Methods Forty-five C57/BL6 male mice were randomly divided into three groups: sham group, IRI group, and IRI+MSCs group, with 15 mice in each group. The IRI-induced AKI model in mice was reproduced by clamping both renal pedicles for 35 minutes. In the sham group, both kidneys were exposed, but their pedicles were not clamped. Six hours after reperfusion, mice in IRI+MSCs group received 100 μL of MSCs (1×104 /μL) isolated from the bone marrow from C57/BL6 mice via tail vein, while the mice in the IRI group received same amount of normal saline. Blood samples were harvested at 48 hours after reperfusion, and levels of serum creatinine (SCr) and blood urea nitrogen (BUN) were determined. The changes in renal pathology were observed by microscopy with PAS staining, and the tubular injury and acute tubular necrosis (ATN) scores were calculated. The number of leukocytes (CD45+) infiltrated in kidney at 24 hours and 72 hours after reperfusion was measured with flow cytometry. The number of neutrophils (Ly-6G+) and macrophages (F4/80+) infiltrated in kidneys at 24 hours and 72 hours after reperfusion was determined by immunofluorescence. Results There was significant increase in the related parameters in IRI group compared with those of sham group. The levels of SCr (μmol/L) and BUN (mmol/L) were 180.3±8.8 vs. 9.7±3.5, and 1 121.1±8.3 vs. 9.4±2.3, both P < 0.01. The score of tubular injury was 4.80±0.55 vs. 0 at 48 hours after reperfusion. The quantity of leukocyte (CD45+) infiltration in kidney at 24 hours and 72 hours after reperfusion was increased (×105 cells/g: 60.50±2.56 vs. 19.46±4.83, 42.00±1.87 vs. 14.70±3.74, both P < 0.01), and the number of neutrophils (Ly-6G+) and macrophages (F4/80+) infiltrated in kidney at 24 hours and 72 hours after reperfusion was also increase although the number of leukocytes infiltrated in kidney was significantly lower at 72 hours after reperfusion than that at 24 hours. There was significant lowering of the levels of SCr and BUN [SCr (μmol/L): 99.0±8.0 vs. 180.3±8.8, BUN (mmol/L): 84.5±7.6 vs. 112.1±8.3, both P < 0.01] in IRI+MSCs group, compared to IRI group. For the degree of tubular necrosis in two groups, the tubular injury scores were 2.60±0.55 vs. 4.80±0.55 (P < 0.05). The number of leukocytes infiltrated in kidney at 24 hours and 72 hours after reperfusion (×105 cells/g) were 24.20±4.53 vs. 60.50±2.56, 31.70±3.15 vs. 42.00±1.87 (both P < 0.01). The number of neutrophils was lowered despite (the number of macrophages was increased). However, the number of infiltrated leukocytes was significantly more in IRI+MSCs group at 72 hours than that at 24 hours (×105 cells/g: 31.70±3.15 vs. 24.20±4.53, P < 0.05). Conclusion MSCs could protect against IRI induced AKI by reducing the total number of leuckocytes, especially that of the neutrophils infiltrating into ischemic kidney and by recruiting macrophages into ischemic kidney.