Molecular imaging with positron emitting tomography (PET) is widely accepted as an essential part of the diagnosis and evaluation of neoplastic and non-neoplastic disease processes. PET has expanded its role from the research domain into clinical application for oncology, cardiology and neuropsychiatry. More recently, PET is being used as a clinical molecular imaging tool in pediatric neuroimaging. PET is considered an accurate and noninvasive method to study brain activity and to understand pediatric neurological disease processes. In this review, specific examples of the clinical use of PET are given with respect to pediatric neuroimaging. The current use of co-registration of PET with MR imaging is exemplified in regard to pediatric epilepsy. The current use of PET/CT in the evaluation of head and neck lymphoma and pediatric brain tumors is also reviewed. Emerging technologies including PET/MRI and neuroreceptor imaging are discussed.