Introduction: In intensity-modulated radiation therapy (IMRT) planning for nasopharyngeal carcinoma (NPC), cervical lymph nodes (CLNs) that appear negative on magnetic resonance imaging (MRI) scans can be difficult to target. The purpose of this study was to assess the advantage of F-18-fluorodeoxyglucose positron emission tomography with computed tomography (F-18-FDG PET/CT) for distinguishing MRI-negative CLNs and the effect of F-18-FDG PET/CT on diagnosis, target delineation, and dose prescription in IMRT planning for NPC. Methods: Thirty-five NPC patients with 37 MRI-negative CLNs underwent 18F-FDG PET/CT imaging before treatment. Ultrasonography-guided fine-needle aspiration cytology (USgFNAC) was performed to examine the pathology of CLNs. The F-18-FDG PET/CT and cytopathological results were compared, and the diagnostic accuracy of F-18-FDG PET/CT was calculated. The cytopathologically confirmed CLNs were delineated and treated as the gross tumor volume of lymph nodes (denoted as GTVnd). Results: Nineteen of the 37 MRI-negative CLNs were positive on F-18-FDG PET/CT, and metastasis was confirmed by USgFNAC in 16 CLNs. Of the remaining 18 F-18-FDG PET/CT-negative lymph nodes, metastasis was confirmed in one. The diagnostic accuracy, sensitivity, and specificity of F-18-FDG PET/CT were 89.2%, 94.1%, and 85.0%, respectively. The positive and negative predictive values were 84.2% and 94.4%, respectively. With a median follow-up of 48.3 months, no relapse was observed among the F-18-FDG PET/CT-positive CLNs with metastasis confirmed by USgFNAC and treated as GTVnd. Conclusion: F-18-FDG PET/CT had high accuracy, sensitivity, and specificity for distinguishing MRI-negative CLNs. F-18-FDG PET/CT-positive CLNs could reasonably be categorized as high-risk clinical tumor volume in IMRT planning for NPC.