Congenital obstructive nephropathy (CON) leads to renal fibrosis and chronic kidney disease. The aim of the study was to investigate the predictive value of urinary endoglin, periostin, cytokeratin-18, and transforming growth factor-β1 (TGF-β1) for assessing the severity of renal fibrosis in 81 children with CON and 60 controls. Children were divided into three subgroups: severe, moderate scars, and borderline lesions based on 99mTc-ethylenedicysteine scintigraphy results. Periostin, periostin/Cr, and cytokeratin-18 levels were significantly higher in the study group compared to the controls. Children with severe scars had significantly higher urinary periostin/Cr levels than those with borderline lesions. In multivariate analysis, only periostin and cytokeratin-18 were independently related to the presence of severe and moderate scars, and periostin was independently related to borderline lesions. However, periostin did not differentiate advanced scars from borderline lesions. In ROC analysis, periostin and periostin/Cr demonstrated better diagnostic profiles for detection of advanced scars than TGF-β1 and cytokeratin-18 (AUC 0.849; 0.810 vs. 0.630; 0.611, respectively) and periostin for detecting borderline lesions than endoglin and periostin/Cr (AUC 0.777 vs. 0.661; 0.658, respectively). In conclusion, periostin seems to be a promising, non-invasive marker for assessing renal fibrosis in children with CON. CK-18 and TGF-β1 demonstrated low utility, and endoglin was not useful for diagnosing advanced scars.