Extrarenal malignant rhabdoid tumor (MRT) is a rare malignancy in childhood and has a poor prognosis. Accurate histopathologic diagnosis and staging of the malignancy has major implications for patient management. The application of F-fluoro-deoxy-glucose positron emission tomography/computed tomography (F-FDG PET/CT) in pediatric malignancy has been well described and is having a significant clinical impact in many common pediatric cancers, in particular lymphoma, brain tumors, bone and soft tissue sarcomas. The use of PET/CT using F-FDG in rare tumors such as MRT is unclear. Two cases of MRT in childhood are described. One patient, a 12-year-old female, was shown to have extensive metastatic disease on PET/CT, showed poor response to chemotherapy and progression of disease detected on PET/CT. Her management was changed to palliative care. The second child, a 20-month-old female, presented with a parapharyngeal mass. The initial magnetic resonance imaging showed the mass and possible metastatic ipsilateral cervical lymph nodes. The initial staging PET/CT confirmed avid metabolic activity in the tumor and regional node involvement but no distant metastases. She showed an initial good but incomplete response on PET/CT and magnetic resonance imaging to chemotherapy and her treatment program was changed. The patient relapsed with recurrent pharyngeal tumor and her management was changed to palliative care. MRT accumulate F-FDG avidly. PET/CT was helpful in the initial staging, assessing response to treatment, and in clinical decisions at various stages of management for both patients.