Children with malignancies undergo recurrent imaging as part of tumor diagnosis, staging and therapy response assessment. Simultaneous positron emission tomography (PET) and magnetic resonance (MR) allows for decreased radiation exposure and acts as a one-stop shop for disease in which MR imaging is required. Nevertheless, PET/MR is still less readily available than PET/CT across institutions. This article serves as a guide to successful implementation of a clinical pediatric PET/MR program based on our extensive clinical experience. Challenges include making scanners more affordable and increasing patient throughput by decreasing total scan time. With improvements in workflow and robust acquisition protocols, PET/MR imaging is expected to play an increasingly important role in pediatric oncology.