We compared the effectiveness technetium-99m methoxyisobutylisonitrile (Tc-99m MIBI) single photon emission computed tomography (SPECT) and magnetic resonance imaging (MRI) of head and neck in evaluating cervical lymph node (LN) metastasis in nasopharyngeal carcinomas (NPC). Forty NPC patients with cervical LN metastases confirmed histopathologically underwent Te-99m MIBI SPECT and MRI of the head and neck to evaluate cervical LN metastases. For 16 LN lesions with discordant results between Tc-99m MIBI SPECT and MRI, Tc-99m MIBI SPECT could correctly detect 1 metastatic and 10 benign LN lesions as well as MRI could correctly detect 3 metastatic and 2 benign LN lesions. Agreement positive results of Tc-99m MIBI SPECT and MRI could correctly detect all of the remaining 24 metastatic LN lesions. Tc-99m MIBI SPECT has a better specificity but a lower sensitivity for detecting cervical LN metastases in NPC when compared with MRI. The combined use of Tc-99m MIBI SPECT and MRI could increase the accuracy compared with the single use of either Te-99m MIBI SPECT or MRI to detect cervical LN metastases in NPC.