Nuclear medicine and molecular imaging have a small but growing role in the management of paediatric and neonatal diseases. During the past decade, combined PET/MRI has emerged as a clinically important hybrid imaging modality in paediatric medicine due to diagnostic advantages and reduced radiation exposure compared to alternative techniques. The applications for nuclear medicine, radiopharmaceuticals and combined PET/MRI in paediatric diagnosis is broadly similar to adults, however there are some key differences. There are a variety of clinical applications for PET/MRI imaging in children including, but not limited to, oncology, neurology, cardiovascular, infection and chronic inflammatory diseases, and in renal-urological disorders. In this article, we review the applications of PET/MRI in paediatric and neonatal imaging, its current role, advantages and disadvantages over other hybrid imaging techniques such as PET/CT, and its future applications. Overall, PET/MRI is a powerful imaging technology in diagnostic medicine and paediatric diseases. Higher soft tissue contrasts and lower radiation dose of the MRI makes it the superior technology compared to other conventional techniques such as PET/CT or scintigraphy. However, this relatively new hybrid imaging has also some limitations. MRI based attenuation correction remains a challenge and although methodologies have improved significantly in the last decades, most remain under development.