In head and neck oncology, the information provided by positron emission tomography (PET)/CT and MRI is often complementary because both the methods are based on different biophysical foundations. Therefore, combining diagnostic information from both modalities can provide additional diagnostic gain. Debates about integrated PET/MRI systems have become fashionable during the past few years, since the introduction and wide adoption of software-based multimodality image registration and fusion and the hardware implementation of integrated hybrid PET/MRI systems in pre-clinical and clinical settings. However, combining PET with MRI has proven to be technically and clinically more challenging than initially expected and, as such, research into the potential clinical role of PET/MRI in comparison with PET/CT, diffusion-weighted MRI (DW MRI) or the combination thereof is still ongoing. This review focuses on the clinical applications of PET/MRI in head and neck squamous cell carcinoma (HNSCC). We first discuss current evidence about the use of combined PET/CT and DW MRI, and, then, we explain the rationale and principles of PET/MR image fusion before summarizing the state-of-the-art knowledge regarding the diagnostic performance of PET/MRI in HNSCC. Feasibility and quantification issues, diagnostic pitfalls and challenges in clinical settings as well as ongoing research and potential future applications are also discussed.