The purpose of this meta-analysis is to determine the efficacy of mesenchymal stromal/stem cell (MSC) transplantation therapy on lupus nephritis (LN) and renal function of patients with systemic lupus erythematosus (SLE). Articles that reported the data of MSC therapy on the renal function as well as disease activity of LN in patients with SLE were searched in PubMed, Web of Science, Embase and the Cochrane Library. Mean difference for disease activity and laboratory parameters were pooled to evaluate the efficacy of MSC, and incidence was pooled for clinical remission, death and severe adverse event. A total of 12 studies with 586 patients were included. The disease activity indices, including SLEDAI and BILAG, were significantly decreased within 12 months after MSC therapy (P< 0.05). Laboratory parameters for renal function and disease control including estimated glomerular filtration rate, creatinine, blood urea nitrogen, complement C3, albumin and urine protein, were also significantly improved after therapy. The pooled rate of clinical remission at 12 months was 28.1% and the total rate during follow-up was 33.7%. The pooled rate of death at 12 months was 5.2% and the total rate during follow-up was 5.5%. Severe adverse events were rare and not associated with the treatment of MSC. This is the first meta-analysis that focuses on the effect of MSC on LN and renal function of patients with SLE, and the results shows a favorable safety profile and encouraging results of MSC for improving the disease activity of LN as well as the renal function of SLE patients.