Mesenchymal stem cells (MSCs), discovered and isolated from the bone marrow in the 1960s and with self-renewal capacity and multilineage differentiation potential, have valuable immunomodulatory abilities. Acute kidney injury (AKI) refers to rapid renal failure, which exhibits as quickly progressive decreasing excretion in few hours or days. This study was performed to assess the efficacy of MSCs in the treatment of AKI induced by ischemia-reperfusion using a meta-analysis method. A literature search using corresponding terms was performed in the following databases: Embase, Cochrane Library, PubMed, and ISI Web of Science databases up to Dec 31, 2019. Data for outcomes were identified, and the efficacy of MSCs for AKI was assessed using Cochrane Review Manager Version 5.3. Nineteen studies were eligible and recruited for this meta-analysis. MSC treatment can reduce the Scr levels at 1 day, 2 days, 3 days, 5 days, and >7 days (1 day: WMD=−0.56, 95% CI: -0.78, -0.34, P<0.00001; 2 days: WMD=−0.58, 95% CI: -0.89, -0.28, P=0.0002; 3 days: WMD=−0.65, 95% CI: -0.84, -0.45, P<0.00001; 5 days: WMD=−0.35, 95% CI: -0.54, -0.16, P=0.0003; and >7 days: WMD=−0.22, 95% CI: -0.36, -0.08, P=0.002) and can reduce the levels of BUN at 1 day, 2 days, 3 days, and 5 days (1 day: WMD=−11.72, 95% CI: -18.80, -4.64, P=0.001; 2 days: WMD=−33.60, 95% CI: -40.15, -27.05, P<0.00001; 3 days: WMD=−21.14, 95% CI: -26.15, -16.14, P<0.00001; and 5 days: WMD=−8.88, 95% CI: -11.06, -6.69, P<0.00001), and it also can reduce the levels of proteinuria at 3 days and >7 days and alleviate the renal damage in animal models of AKI. In conclusion, MSCs might be a promising therapeutic agent for AKI induced by ischemia-reperfusion.