Background: The aim of this study was to investigate novel urinary biomarkers including N-acetyl-β-d-glucosaminidase (NAG), neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1), and liver-type fatty acid binding protein (L-FABP) in children with β-thalassemia major (β-TM). Materials and methods: Totally, 52 patients (29 boys, 23 girls) with β-TM and 29 healthy controls (3–17 years) were included. Various demographic characteristics and blood transfusions/year, disease duration, and chelation therapy were recorded. Serum urea, creatinine, electrolytes, and ferritin and urinary creatinine, protein, calcium, phosphorus, sodium, potassium, and uric acid in first morning urine samples were measured and estimated glomerular filtration rate (eGFR) was calculated. Routine serum and urinary biochemical variables, urinary NAG to Creatinine (UNAG/Cr), UNGAL/Cr, UKIM-1/Cr, and UL-FABP/Cr ratios were determined. Results: Patients had similar mean serum urea, creatinine and eGFR levels compared with controls (p > 0.05 for all). The mean urinary protein to creatinine (UProtein/Cr) ratio was significantly higher in patients compared to the healthy subjects (0.13 ± 0.09 mg/mg and 0.07 ± 0.04 mg/mg, respectively; p < 0.001). Significantly increased UNAG/Cr (0.48 ± 0.58 vs. 0.23 ± 0.16, p = 0.026) and UNGAL/Cr (22.1 ± 18.5 vs. 11.5 ± 6.17, p = 0.01) ratios were found in β-TM patients compared with healthy controls. However, no differences were found in serum and urinary electrolytes or UKIM-1/Cr and UL-FABP/Cr ratios between patients and controls (p > 0.05). Significant correlations were found between urinary biomarkers and urinary electrolytes (p < 0.05). Conclusions: Our results suggest that urinary NAG and NGAL may be considered to be reliable markers to monitor renal injury in β-TM patients.