Background Ureteropelvic junction stenosis (UPJS) is the most common cause of clinically significant antenatal hydronephrosis. We compared separate renal function results obtained using technetium-99m-mercaptoacetyltriglycine (Tc-99m MAG-3) and technetium-99m-dimercaptosuccinic acid (Tc-99m DMSA) in pediatric patients with UPJS to evaluate the adequacy of Tc-99m MAG-3 scintigraphy and the necessity of additional Tc-99m DMSA scintigraphy during follow-up. Methodology Patients diagnosed with hydronephrosis in the Pediatric Nephrology Department of Pamukkale University Faculty of Medicine over a period of 10 years (2012-2022) were evaluated retrospectively. Patients who had been diagnosed with UPJS and underwent both Tc-99m MAG-3 and Tc-99m DMSA scintigraphy during follow-up were included in the study. Technetium-99m-labeled MAG-3 and DMSA scans were re-evaluated for all patients by the Department of Nuclear Medicine. Results The study included 52 children with unilateral UPJS (12 girls and 40 boys) with a mean age of 6.34 ± 4.81 years (range: 2.97-9.79 years). Thirty-six patients (69.2%) were diagnosed antenatally. Differential renal function in Tc-99m DMSA was 46.94 ± 10.64 and in Tc-99m MAG-3 was 43.08 ± 11.18; the functions were lower in Tc-99m MAG-3, but the values were within normal limits for both groups (p=0.0001, z=-3.893). When differential renal functions were compared between Tc-99m DMSA and Tc-99m MAG-3 results, a statistically significant positive and strong correlation was found in the kidney with ureteropelvic junction obstruction (UPJO) (p=0.0001, r=0.752). When classifying the Tc-99m MAG-3 and Tc-99m DMSA results in the kidney with UPJO (supranormal, normal, low function) for the determination of differential renal functions, there was a consistency of 76%, and it was correlated (p=0.0001, k=0.456). While two patients had supranormal function and 13 patients had low function in Tc-99m MAG-3, five patients had supranormal function, and eight patients had low function in Tc-99m DMSA. Conclusions Some studies in the literature have reported that Tc-99m MAG-3 causes supranormal function measurements in patients with UPJS; our results showed that Tc-99m DMSA resulted in a higher rate of supranormal values for affected kidneys. We believe that Tc-99m DMSA should not be performed in addition to Tc-99m MAG-3 scintigraphy in the follow-up of every patient with UPJS but can be utilized in select cases, such as patients with surgical indications and those suspected before surgery.