Objective The aim of this meta-analysis was to evaluate the therapeutic effects of mesenchymal stem cells (MSCs) versus other regimens as induction therapy in kidney transplantation patients.Methods PubMed, Embase, EBSCO, Ovid and the Cochrane Library were searched to identify prospective clinical trials which compared MSCs with other regimens as induction therapy in renal allograft.Results Four studies with five cohorts were contained, including a total of 301 patients. The pooled results revealed that the MSCs therapy had a lower 1-year infection rate (RR=0.73, 95% CI: 0.58–0.93, P=0.01), espeicially for 1-year opportunistic infection rate (RR=0.59, 95% CI: 0.37–0.93, P=0.02). There were no significant differences between the two protocols regarding 1-year acute rejection (AR) rate (RR=0.69, 95% CI: 0.42–1.14, P=0.15), 1-year graft survival rate (RR=0.99, 95% CI: 0.95–1.03, P=0.74), delayed graft function (DGF) rate (RR=0.72, 95% CI: 0.34–1.50, P=0.38) and renal graft function at 1 month (MD=2.4, 95% CI: -7.41– 12.22, p=0.63), 3 months (MD=0.91, 95% CI: -4.17– 5.98, p=0.73), 6 months (MD=-1.41, 95% CI: -5.69– 2.87, p=0.52), 12 months (MD=1.25, 95% CI: -3.89– 6.4, p=0.63) post surgery. Subgroup analysis demonstrated 1-year AR rate, DGF rate and renal graft function at 12 month post surgery did not reach to a significant difference between low-dose calcineurin inhibitors (CNIs) group with standard-dose CNIs group, indicating successful CNIs withdrawal in combination with MSCs treatment. Meanwhile, when applied MSCs as an alternative standard induction therapy regimen, all of those outcomes mentioned above were also comparable with those in MSCs plus standard induction therapy group.Conclusion Induction therapy of MSCs has similar inducing immune tolerance effects on the recipients in kidney transplantation compared with that of other regimens. However, regarding the long term effect, as represented by 1-year infection rate, 1-year opportunistic infection rate and CNIs withdrawl, MSCs therapy has a significant advantage.