There are limited data on the risk factors for chronic kidney disease (CKD) in children with idiopathic nephrotic syndrome (INS). This retrospective cohort study aimed to develop a predictive model for CKD progression in children with INS. Between 1970 and 2012, a total of 294 patients with INS were followed up. The primary outcome was progression to CKD stage 3 or higher. A predictive model was developed using a Cox proportional hazards model. A score was calculated using b-coefficients and summing up points assigned to each significant variable. Prognostic score was grouped into categories: low risk, medium risk, and high risk. Median follow-up was 6.9 years. Median renal survival was 26.1 years and probability of CKD stage 3 or higher was 8 % in 10 years. Multivariate analysis showed that the most accurate model included initial age, hematuria, and steroid resistance. Accuracy was high with a c-statistic of 0.95 (95 % confidence interval [CI] 0.91–0.99), 0.92 (95 % CI 0.88–0.96), and 0.92 (95 % CI 0.87–0.97) at 2, 5, and 10 years of follow-up respectively. By survival analysis, 10-year renal survival was 100 % for the low-risk and 95 % for the medium-risk group, while 40 % of high-risk patients would exhibit CKD stage 3 or higher (P < 0.001). Our predictive model of CKD may contribute to the early identification of a subgroup of INS patients at a high risk of renal dysfunction.