The usefulness of PET/MRI in head and neck malignancy has not been fully elucidated. The purpose of our study was to evaluate the diagnostic accuracy and confidence of PET/MRI in comparison with PET or MRI alone. This study included 73 consecutive patients who underwent [18F] FDG PET/MRI in head and neck under the suspicion of malignancy. A neuroradiologist and a nuclear medicine specialist reviewed MRI and PET images, respectively and independently, followed by a consensus review of PET/MRI one month later. For 134 lesions, accuracy and confidence were compared among PET, MRI, and PET/MRI. For lesion base, PET/MRI had a sensitivity of 85.7%, a specificity of 89.1%, a PPV of 89.6%, a negative predictive value of 85.1%, and an accuracy of 87.3%. AUCs of PET/MRI per lesion (0.926) and per patient (0.934) for diagnosing malignancy were higher than PET (0.847 and 0.747, respectively) or MRI (0.836 and 0.798, respectively) alone (P < 0.05). More than 80% of the cases (111/134) showed diagnostic concordance between PET and MRI. PPV of PET/MRI was higher in malignant concordant cases (93.2%, 55/59) than in discordant cases (62.5%, 5/8) (p = 0.040). Confident scoring rate in malignant concordant cases was higher on PET/MRI (96.6%, 57/59) than on MRI (76.3%, 45/59) (p = 0.003). In conclusion, compared with PET or MRI alone, PET/MRI presents better diagnostic performance in accuracy and confidence for diagnosis of malignancy. PET/MRI is useful in patients with head and neck cancer.