Background/Objectives: Fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT) is a valuable imaging modality for detecting malignancies and diagnosing fever of unknown origin (FUO). However, data regarding FDG accumulation in bone marrow among pediatric acute leukemia (AL) cases are limited. In this study, we aimed to compare FDG-PET/CT findings between children with AL and those with inflammatory diseases (IDs), including FUO, and develop a scoring system for differential diagnoses. Methods: We retrospectively analyzed FDG-PET/CT findings in six children with AL and 22 with IDs. The maximum standardized uptake value (SUV max), visual score (VS), and spread score (SS) were evaluated across various bone marrow sites, including vertebrae, pelvic bone, humerus, forearm, and femur. Statistical analysis consisted of Mann–Whitney U test for group comparisons and receiver operating characteristic curve (ROC)/area under the curve (AUC) analyses to assess diagnostic performance. Results: SUV max, VS, and SS were significantly higher in children with AL across all evaluated sites. The combined VS + SS scoring system yielded the highest diagnostic accuracy. A simplified version using only the VS of the middle humerus and femur plus the SS showed comparable effectiveness. Conclusions: FDG-PET/CT in children with AL showed high FDG accumulation in bone marrow areas in the whole body. The simple scoring system, which comprises FDG accumulation in the middle portion of the extremities and the whole body, appears to be helpful in distinguishing AL from IDs in children. FDG-PET/CT-based visual scoring may provide supportive information alongside conventional diagnostics in pediatric acute leukemia.