Objectives: Chronic kidney diseases (CKD) often progress to end-stage kidney disease. However, the progression rate of CKD varies among patients, especially in children. A significant number of pediatric CKD are caused by congenital anomalies of the kidney and urinary tract (CAKUT), and its progression is hard to predict. Here, we report our search for urinary biomarkers to predict the progression of CKD in this population. Methods: We selected 25 patients with CAKUT (kidney hypoplasia (H, n=12) or reflux nephropathy (R, n=13)) from the pediatric prospective cohort study KNOW-Ped CKD (KoreaN cohort study for outcomes in patients with pediatric CKD), and grouped into the fast (F) and slow (S) progression groups (an annual eGFR decline ≥ 5 vs. < 5 mL/min/1.73 m2). Baseline characteristics of eGFR, proteinuria, hypertension, and age were comparable between the groups. Urine samples were analyzed using capillary electrophoresis-mass spectrometry.  Results: In total, 2,041 proteins were identified, and 71 as the 1st targeted proteins (valid value > 70%, permutation FDR < 0.05, log2 fold change ± 1.5). In the RF group, 45 proteins including epidermal growth factor, collagen type XIV α1 chain, tenascin-X, and Ephrin type-B receptor 4 were significantly down-regulated compared with the RS group. Five proteins including Apolipoprotein A-II more abundant in the RF group. In the HF group, four proteins including Triosephosphate isomerase were significantly down-regulated, and 17 proteins, including the collagen type VI α1 chain were up-regulated than the HS group. In biological pathway analysis, angiogenesis pathway was deactivated in the RF group. The collagen catabolic process and polarized epithelial cell differentiation pathway were activated in the HF group, whereas NADH regeneration and glycolytic process were associated with slow progression.  Conclusions: We found several differentially regulated peptides according to progression rate and underlying diseases. Upon validation, these might be candidates of biomarkers predicting the progression of CKD.