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Developing a new reliable prognostic marker to predict the prognosis and supply better and more suitable therapy for patients with nasopharyngeal carcinoma (NPC) is urgent. Therefore, we performed this systematic review of the literature with meta-analysis to clarify and explore the associate expression of nm23-H1 with prognosis of NPC patients.Literature research in Cochrane Library, PubMed, and EMBASE was performed up to July 2016. Eligible case–control studies of associate expression of nm23-H1 with prognosis of NPC patients were included.Nine studies met our inclusion criteria and were finally included for the analysis, involving 861 participants. Our meta-analysis revealed that the low expression of nm23-H1 in NPC was: RR = 2.13, 95% CI 1.15–3.95 and R = 2.56, 95% CI 2.03–3.22; and poorer overall survival (OS) rate was 3-year OS rate: RR: 0.55; 95% CI: 0.45–0.67 and 5-year OS rate: RR: 0.60; 95% CI: 0.52–0.69. Furthermore, the statistical significance was constant irrespective of different NPC subtypes.The low expression of nm23-H1 is associated with poorer prognosis in patients with NPC, suggesting that it is a prognostic factor and potential biomarker for survival in NPC.