This prospective study aimed to evaluate the characteristics and findings of children who presented with acute pyelonephritis (APN) and to determine the independent risk factors for kidney scarring. Patients who satisfied the following criteria were enrolled in the study: first known episode of APN; at least two of the following findings: fever ≥ 38.5 °C, white blood cell count ≥ 10,000/mm3, erythrocyte sedimentation rate ≥ 20 mm/h, C-reactive protein ≥ 20 mg/dL; absence of congenital abnormalities or other kidney and systemic diseases, except vesicoureteral reflux (VUR); no APN relapses until the time of kidney scar detection. 99mTc-Dimercaptosuccinic acid kidney scintigraphy (99mTc-DMSA) was performed at admission, along with a kidney ultrasound. Follow-up 99mTc-DMSA took place after 6 months. Radiographic cystourethrography for VUR detection and grading was performed 1 month after the acute infection. We enrolled 70 children in the study. The kidney ultrasound failed to diagnose more than half of the cases of APN. VUR was found in 21.5% of children. 75% had findings of APN in the acute phase through 99mTc-DMSA, while in the second 99mTc-DMSA, there was a complete remission in 68% of them. Scars were observed more frequently in older children, children with VUR grade ≥ III, and children not on antibiotic prophylaxis. VUR did not appear to be associated with the first episode of APN, and children older than 1 year of age had a higher risk of scarring. Antibiotic prophylaxis may prevent kidney scarring due to host immunomodulatory effects, but more studies are needed so that conclusions can be drawn.