Background: The bones are the most common site of distant metastasis in nasopharyngeal carcinoma (NPC). Few prognostic markers are available to guide treatment and sub-classify patients with bone metastasis. We aimed to identify the prognostic value of pretreatment serum alkaline phosphatase (ALP) and plasma Epstein-Barr virus DNA (EBV DNA) in patients with bone-only metastasis. Methods: A total of 272 patients who developed bone-only metastases after therapy were retrospectively analyzed. Patients were categorized according to pretreatment serum ALP (< or >= 110 U/L) and pretreatment plasma EBV DNA (< or >= 6,750 copies ml(-1)). Univariate and multivariate analyses of clinical variables were performed using Cox proportional hazards regression models. Overall survival (OS) was analyzed using the Kaplan-Meier method and compared using the log-rank test. Results: Median OS for the cohort was 34.06 months (range, 2.53-143.87 months). Multivariate Cox proportional hazard analysis verified pretreatment serum ALP and pretreatment plasma EBV DNA were independent prognostic factors for OS. In stratified survival analysis of patients with elevated pretreatment serum ALP and/or plasma EBV DNA, delivery of radiotherapy (RT) to bone metastases provided a significant OS benefit compared to other therapeutic methods (P < 0.05). Conclusions: This study demonstrates two important points: firstly, pretreatment serum ALP and plasma EBV DNA have prognostic value at the first diagnosis of bone-only metastasis in NPC. Secondly, radiotherapy of bone metastasis improves the prognosis of patients with elevated pretreatment serum ALP and plasma EBV DNA.