The aims of our study were to compare F-18 fluorodeoxyglucose (FDG) positron-emission tomography/magnetic resonance imaging (PET/MRI) and PET/computed tomography (CT) in pediatric oncology patients in terms of anatomic correlation of FDG-positive lesions, and also to compare diffusion-weighted imaging (DWI) with PET to assess the correlation between apparent diffusion coefficient (ADC) values and standardized uptake value (SUV). Sequential PET/CT and PET/MRI images and/or whole-body DWI and ADC mapping in 34 pediatric patients were retrospectively analyzed. FDG-positive lesions were visually scored for CT, T1-weighted, T2-weighted, and DWI images separately in terms of anatomic correlation of FDG-avid lesions. Correlation analysis was performed for SUV parameters and ADC values. Among 47 FDG-positive lesions identified concurrently on PET/CT and PET/MRI, 37 were positive on CT and 46 were positive on at least one MRI sequence (P=0.012). Among 32 FDG-positive lesions for which DWI were available, 31 could be clearly depicted on DWI, resulting in significant difference compared with CT alone in the detection of FDG-positive lesions. No correlation was found between ADC and SUV. FDG PET/MRI exhibits better performance than PET/CT in terms of anatomic correlation of FDG-avid lesions. Therefore, PET/MRI may be more advantageous than PET/CT, not only due to reduced ionizing radiation dose but also for a better depiction of FDG-avid lesions in pediatric PET imaging.