Background: 99mTc-labelled methylene diphosphonate (99mTc-MDP) uptake can diagnose bone metastasis in patients. The purpose of our study was to assess the additional value of single photon emission computed tomography/computed tomography (SPECT/CT) over whole-body planar scintigraphy (WBS) and SPECT in detecting bone lesions in nasopharyngeal carcinoma patients.Methods: Data from 126 patients (169 lesions) with nasopharyngeal carcinoma who underwent WBS, SPECT, and SPECT/CT in this 2-year prospective study. These scans of patients were directly compared for detection and characterization of bone lesions. McNemar’s multistep analysis was performed in patient-based and lesion-based.Results: On patient-based analysis, SPECT/CT significantly reduced the number of equivocal diagnosis than WBS and SPECT (p<0.004), and SPECT significantly reduced the number of equivocal diagnosis than WBS (p<0.004). The diagnostic coincidence rate of SPECT/CT (90.2%) is significantly higher than WBS (45.5%) and SPECT (61.6%). On lesion-based analysis, SPECT/CT significantly decreased the number of equivocal lesions than WBS and SPECT. SPECT/CT interpretation revealed 98 benign lesions and 37 malignant lesions, more than WBS and SPECT. For all the 112 patients, 32 equivocal patients were diagnosed definitely based on SPECT/CT findings, and received specific treatment and management.Conclusion: SPECT/CT can add incremental value to whole‑body bone imaging by significantly improves diagnostic sensitivity in nasopharyngeal carcinoma patients and decrease the number of equivocal lesions that do not contribute to diagnosis. Moreover, SPECT/CT can contribute to change the clinical management of patient and identify a more accurate metastatic range.