In pediatric patients with hydronephrosis, differentiating true ureteropelvic junction obstruction (UPJO) from non-obstructive dilation (NOD) using ultrasound alone poses significant challenges. While renography can indicate obstructive voiding patterns and assess differential renal function (DRF), it is an invasive procedure. This study aims to evaluate the effectiveness of urinary biomarkers as a non-invasive alternative to accurately predict UPJO in patients with unilateral hydronephrosis. An Institutional Review Board (IRB)-approved study enrolled 81 hydronephrotic patients and 14 healthy controls, excluding those with bilateral high-grade hydronephrosis, chronic renal disease, or those on immunosuppressant therapy. The hydronephrotic patients were classified into UPJO and NOD groups based on their progression to pyeloplasty. Urine samples were analyzed for Neutrophil Gelatinase-Associated Lipocalin (NGAL), Human Carbohydrate Antigen 19-9 (HCA19-9), Interferon-Gamma Inducible Protein 10 kDa (IP10), and Monocyte Chemoattractant Protein 1 (MCP1) using enzyme-linked immunosorbent assay (ELISA). The results indicated that UPJO patients had significantly elevated levels of NGAL, HCA19-9, and IP10 compared to those with NOD. Additionally, patients with decreased DRF showed significantly higher levels of NGAL and HCA19-9. The logistic regression model, utilizing all urinary biomarker levels, achieved a sensitivity of 94.29% and an area under the curve of 0.91, indicating high predictive accuracy. Notably, among younger patients aged 0-3, those with UPJO exhibited higher levels of HCA19-9 and IP10 than neonates with NOD. This study represents the largest pediatric cohort examining urinary biomarkers in unilateral hydronephrosis, demonstrating that elevated biomarker levels correlate with UPJO and impaired renal function, highlighting their potential in clinical practice.