The aim of this study was to explore the influences of age-matched control and/or age-specific template on voxel-wise analysis of brain F-18-fluorodeoxyglucose positron emission tomography (F-18-FDG PET) data in pediatric epilepsy patients. We, retrospectively, included 538 pediatric (196 females; age range of 12 months to 18 years) and 35 adult subjects (18 females; age range of 20-50 years) without any cerebral pathology as pediatric and adult control group, respectively, as well as 109 pediatric patients with drug-resistant epilepsy (38 females; age range of 13 months to 18 years) as epilepsy group. Statistical parametric mapping (SPM) analysis for F-18-FDG PET data of each epilepsy patients was performed in four types of procedures, by using age-matched controls with age-specific template, age-matched controls with adult template, adult controls with age-specific template or adult controls with adult template. The numbers of brain regions affected by artifacts among these four types of SPM analysis procedures were further compared. Any template being adopted, the artifacts were significantly less in SPM analysis procedures using age-matched controls than those using adult controls in each age range (p < .001 in each comparison), except in the age range of 15-18 (p > .05 in each comparison). No significant difference was found in artifacts, when compared procedures using the identical control group with different templates (p = 1.000 in each comparison). In conclusion, the age stratification for age-matched control should be divided as many layers as possible for the SPM analysis of brain F-18-FDG PET images, especially in pediatric patients <= 14-year-old, while age-specific template is not mandatory.