Positron-emission tomography/computed tomography (PET/CT) has been proposed as a means to enhance the pretreatment evaluation of cervical lymph node status in patients with nasopharyngeal carcinoma (NPC). We conducted a prospective study to compare PET/CT and enhanced CT for the detection of retropharyngeal lymph node (RLN) metastasis in NPC, and to ascertain the factors that affect its diagnostic performance. Our study population was made up of 33 patients—24 men and 9 women, aged 30 to 81 years (mean: 52)—with newly diagnosed NPC who had been treated over a 2-year period. All patients underwent enhanced CT first, followed by unenhanced 18F-fluorodeoxyglucose (FDG) PET/CT. The detection rate of RLN metastasis on PET/CT was significantly lower than that on enhanced CT (36.4 vs. 75.8%; p < 0.001). A total of 25 of 26 nodes with a discordant finding were negative on PET/CT; they included 13 metastatic lymph nodes with low FDG uptake, 9 that were located close to the primary tumor, 2 that were confluent RLNs, and 1 that was adjacent to the physiologic FDG-avid prevertebral muscle. The maximum standardized uptake value (SUVmax) of RLNs was positively correlated with the minimum axial diameter (r = 0.803, p < 0.001). The PET/CT detection rate was 0% for lymph nodes smaller than 5 mm, 9% for those 5 to 10 mm, and 73% for those 1 cm or larger. The detection rate of PET/ CT at level C1 was significantly lower than that at C2 (22 vs. 67%; p = 0.035). We conclude that unenhanced PET/CT is markedly inferior to enhanced CT for detecting RLN metastasis in NPC, especially in lymph nodes with a minimum axial diameter of less than 1 cm and those in proximity to the primary tumor. Using enhanced CT in PET/CT is justified to improve the recognition of RLN metastasis in patients with NPC.