Although, most patients respond initially to therapy for nephrotic syndrome, about 70% of patients have a relapse. Currently, there is no consensus about the most appropriate second-line agent in children who continue to suffer a relapse. This network meta-analysis was designed to compare the efficacy and safety of the commonly used immunosuppressive agents in second-line therapeutic agents (ie, cyclophosphamide, cyclosporine, tacrolimus and mycophenolate mofetil) for refractory childhood nephrotic syndrome. MEDLINE, Cochrane, EMBASE and Google Scholar databases were searched until October 17, 2015 using the following search terms: cyclophosphamide, cyclosporine, tacrolimus, mycophenolate mofetil and childhood nephrotic syndrome. Randomized controlled trials, prospective 2-arm studies and cohort studies were included. 7 studies with 391 patients were included. Bayesian network meta-analysis found that treatment with mycophenolate mofetil had the greatest odds of relapse compared with tacrolimus (pooled OR=49.72, 95% credibility interval (CrI) 1.65 to 2483.32), cyclophosphamide (pooled OR=72.05, 95% CrI 1.44 to 13633.33) and cyclosporine (pooled OR=11.42, 95% CrI 1.03 to 131.60). Rank probability analysis found cyclophosphamide was the best treatment with the lowest relapse rate as compared with other treatments (rank probability=0.58), and tacrolimus was ranked as the second best (rank probability=0.38). Our findings support the use of cyclophosphamide and tacrolimus in treating children with relapsing nephrotic syndrome.