Abstract Purpose The purpose of this study was to compare the diagnostic accuracies of CT and MR imaging for the detection of metastatic retropharyngeal lymph nodes (RLNs) in patients with nasopharyngeal and oropharyngeal squamous cell carcinoma (SCC). Materials and methods The study included 38 patients (28 men and 10 women; mean age, 65 years; age range, 48–82 years) with nasopharyngeal (n=15) and oropharyngeal (n=23) SCC who underwent both contrast-enhanced CT and MR imaging before chemoradiotherapy. RLNs were classified as malignant or benign on the basis of the results of follow-up MR imaging. Two radiologists independently evaluated the images for diagnosing metastatic RLNs. Results Among a total of 68 RLNs (minimum diameter, ≥4mm) that were detected on gadolinium-enhanced fat-suppressed T1-weighted images, 30 (44%) were malignant and 38 (56%) were benign. The sensitivities of CT versus MRI were 60% versus 97% for observer 1 (p<0.01) and 37% versus 90% for observer 2 (p<0.01). The specificities of CT versus MRI were 92% versus 97% for observer 1 (p=0.50) and 92% versus 100% for observer 2 (p=0.25). The areas under the receiver operating characteristic curve (AUC) for CT versus MRI were 0.788 versus 0.996 for observer 1 (p<0.01) and 0.693 versus 0.961 for observer 2 (p<0.01). Conclusion MR imaging was superior to CT for the detection of metastatic RLNs.