Study has shown that stem cell based therapies are promising strategies in the treatment of several chronic diseases, but their overall benefit in the treatment of diabetic nephropathy (DN) remains controversial. The purpose of this study is to summarize the evidence of the effect of cell-based therapy in the treatment of DN to guide future clinical trials. We searched PubMed, EmBase, and the Cochrane Library for studies from the inception of cell-based therapies up to July 2015. We included animal trials that reported the effects of cell-based therapy on kidney function, cardiovascular risk factors, and body factors. A random-effects model was used to process the data, and the standard mean difference (SMD) was used to evaluate the efficacy of cell-based therapy. We included eight studies that reported data on 159 mice. Overall, we noted that cell-based therapies were associated with significantly reduced plasma creatinine level (P = 0.003), glomerular filtration rate (P < 0.001), plasma glucose level (P = 0.004), serum cholesterol level (P = 0.010), serum triglyceride level (P = 0.032), plasma urea level (P < 0.001), proteinuria (P = 0.008), and Cl fractional excretion (P = 0.023). Furthermore, cell-based therapies were associated with lower kidney weight (P = 0.003), and kidney/body weight (P = 0.004). A sensitivity analysis suggested that cell-based therapy might play an important role in increased body weight. In conclusion, cell-based therapies significantly improve kidney function, cardiovascular risk factors, and body factors in the treatment of DN.