Background: Obstructive congenital anomalies of the kidney and urinary tract have a high risk of kidney failure if not surgically corrected. Dynamic renal scintigraphy is the gold standard technique to evaluate drainage curves and split renal function (SRF). Objectives: To compare functional magnetic resonance (MR) urography with dynamic renal scintigraphy in measuring volumetric SRF and in the classification of drainage curves in patients with congenital anomalies of the kidney and urinary tract. Materials and Methods: We retrospectively collected patients with hydroureteronephrosis or pelvicalyceal dilatation at renal ultrasound, who underwent both functional MR urography and dynamic renal scintigraphy (DRS) within 6 months. DRS studies were evaluated by a single nuclear medicine physician with a double reading. Functional MR urography renograms were blind evaluated twice by two radiologists. The functional MR urographyintra- and inter-reading agreements as well as the agreement between the two imaging techniques were calculated. SRF was evaluated by Area Under the Curve and Rutland-Patlak methods. Drainage curves were classified as normal, borderline or accumulation patterns by both the techniques. Results: Fifty-two children were studied, 14 with bilateral involvement. A total of 104 kidney-urinary tracts were considered: 38 normal and 66 dilated. Considering Area Under the Curve and Rutland-Patlak for SRF, the intra- and inter-reader agreements of functional MR urography had excellent and good results, respectively, and the two techniques demonstrated a good concordance (r2: 67% for Area Under the Curve and 72% for Rutland-Patlak). Considering drainage curves, the inter-readers agreement for functional MR urography and the concordance between the two techniques were moderate (Cohen's k, respectively, 55.7 and 56.3%). Conclusions: According to our results, there are no significant differences between functional MR urography and DRS in measuring volumetric SRF and in the classification of drainage curves in patients with congenital anomalies of the kidney and urinary tract.