Background: Little is known about the nature of metastasis to small cervical lymph nodes (SCLNs) in the patients with nasopharyngeal carcinoma (NPC) examined by using 18-fluoro-2-deoxy-glucose (F-18-FDG) positron emission tomography/computed tomography (PET/CT). The present study aimed to evaluate the diagnostic values of PET/CT in identifying metastasis in SCLNs in NPC patients. Methods: Magnetic resonance images (MRI) and PET/CT scans for 470 patients with newly diagnosed, non-distant metastatic NPC were analyzed. Metastatic rates of SCLNs were defined by the positive number of SCLNs on PET/CT scans and total number of SCLNs on MRI scans. Receiver operating characteristic curve was applied to compare PET/CT-determined stage with MRI-determined stage. Results: In total, 2082 SCLNs were identified, with 808 (38.8%) >= 5 and < 6 mm in diameter (group A), 526 (25.3%) >= 6 and < 7 mm in diameter (group B), 374 (18.0%) >= 7 and < 8 mm in diameter (group C), 237 (11.4%) >= 8 and < 9 mm in diameter (group D), and 137 (6.5%) >= 9 and < 10 mm in diameter (group E). The overall metastatic rates examined by using PET/CT for groups A, B, C, D, and E were 3.5%, 8.0%, 31.3%, 60.0%, and 83.9%, respectively (P < 0.001). In level IV/Vb, the metastatic rate for nodes >= 8 mm was 84.6%. PET/CT examination resulted in modification of N category and overall stage for 135 (28.7%) and 46 (9.8%) patients, respectively. The areas under curve of MRI-determined and PET/CT-determined overall stage were 0.659 and 0.704 for predicting overall survival, 0.661 and 0.711 for predicting distant metastasis-free survival, and 0.636 and 0.663 for predicting disease-free survival. Conclusions: PET/CT was more effective than MRI in identifying metastatic SCLNs, and the radiologic diagnostic criteria for metastatic lymph nodes in level IV/Vb should be re-defined.