The present study aimed to assess the performance of positron emission tomography‑magnetic resonance imaging (PET/MR) for the visualization and characterization of lesions. In addition, the present study investigated whether the apparent diffusion coefficient (ADC) and intravoxel incoherent motion parameters exhibited any significant correlation with standardized uptake values (SUV) in patients with nasopharyngeal carcinoma (NPC). A total of 35 patients with NPC underwent whole body PET‑computed tomography (CT) and head and neck MR imaging (MRI) scans using the PET/CT‑MRI system. Image quality, lesion conspicuity and the diagnostic confidence of PET/CT, T1 weighted (T1w) PET/MR and T2w PET/MR imaging were assessed. The true diffusion coefficient (D), the pseudo‑diffusion coefficient or diffusion within the microcirculation (D*), and the perfusion fraction or the contribution of water moving in the capillaries (f), and ADC, were calculated. The correlation between the ADC, D*, D and f values and the SUV were analyzed using Pearson's correlation analysis. Similar image quality was obtained using PET/CT, T1w PET/MR and T2w PET/MR imaging. However, the T1w PET/MR and T2w PET/MR imaging were more effective than PET/CT in analyzing the lesion conspicuity of the primary tumors and lymph nodes. In addition, T2w PET/MR imaging was more efficient than T1w PET/MR imaging in analyzing primary tumors and lymph nodes. Pearson's correlation analysis showed no significant correlation between the SUV and ADC, and D*, D and f values in NPC. The present results suggested that the application of PET/MR is feasible and could serve as a reliable alternative to PET/CT, while SUV and ADC, D*, D and f values were identified as independent biomarkers in NPC.