Background: Early predictive biomarkers for the diagnosis and management of febrile urinary tract infections (UTIs) can be valuable in children. Methods: Seventy-three patients with febrile UTIs (46 acute pyelonephritis [APN] and 27 lower UTIs), and 56 healthy children were enrolled. Urine levels of neutrophil gelatinase-associated lipocalin (uNGAL) and kidney injury molecule-1 (uKIM-1) and serum levels of cystatin C (sCysC) were measured. Results: uNGAL/creatinine (Cr) and uKIM-1/Cr were higher in the UTI group than those in the controls (p<0.05). uNGAL/Cr and sCysC also increased in patients with APN compared to those with lower UTIs (p<0.05). uNGAL/Cr levels in both the APN and UTI groups decreased after antibiotic treatment, compared to those before treatment (p< 0.05). uNGAL/Cr was correlated with serum levels of white blood cells, C-reactive protein, CysC, and uKIM-1/Cr (p< 0.05). uKIM-1/Cr was also correlated with sCysC (p<0.05). Receiver operating curve analyses showed a good diagnostic profile of uNGAL/Cr and uKIM-1/Cr for identifying UTI (areas under the curves [AUCs], 0.9 and 0.66, respectively) and of uNGAL/Cr and sCysC for predicting APN (AUCs, 0.78 and 0.72, respectively). Conclusions: uNGAL, uKIM-1, and sCysC may be useful for predicting and managing febrile UTIs in children.