The nuclear medicine procedures 99m Tc-ECD SPECT and 18 F-FDG PET play an important diagnostic role in children with refractory seizures. In select patients, surgical removal of epileptogenic cortex is a therapeutic option. Magnetic resonance imaging (MRI) is the principal imaging method used to identify which patients would benefit from the surgery. However, there are cases when MRI does not detect an abnormality (MRI-negative epilepsy). Under these, and other circumstances, functional nuclear medicine studies are helpful in the workup of these patients. A combination of nuclear medicine procedures with MRI and CT depicts functional-anatomic relationships and assists in the non-invasive localization of epileptogenic cortex. Information derived from these procedures is valuable in the selection of candidates for surgical resection. Timing of tracer administration in relation to imaging and monitoring the state of brain activation are essential for accurate interpretation. Ictal and interictal perfusion single photon computed tomography (SPECT), with digital subtraction and registration to MRI can define the region of ictal cortical hyperperfusion more clearly than separate image interpretation. Ictal SPECT is more sensitive than interictal positron emission computed tomography (PET) and interictal PET is more sensitive than interictal SPECT. Interictal SPECT and PET are easier to obtain than ictal SPECT, since they do not require coordination between seizure onset and tracer administration. When surface electrode grids or depth electrodes are planned, anatomic-functional images can assist in their anatomic positioning. The best results are obtained when the planning, execution and interpretation of nuclear medicine procedures are carried out with the support of a well-trained multidisciplinary team familiar with children and refractory seizures.