Background: Increasing evidence indicated that aberrant expression of long noncoding RNAs (lncRNAs) are involved in tumorigenesis and progression of nasopharyngeal carcinoma (NPC). The purpose of this study is to construct a lncRNA-mediated ceRNA network based on Weighted correlation network analysis (WGCNA) and explore the relationship between the constituents of the ceRNA network and the prognosis of patients with NPC.Methods: In this study, WGCNA was performed on the GSE102349 to find modules of highly correlated genes. The preservation of the modules was examined by GSE68799. GSE12452 was utilized to identify the differentially expressed lncRNAs and mRNAs. GSE32960 was utilized to identify the differentially expressed miRNAs. Through annotation and intersection, the lncRNAs and mRNAs in the same WGCNA modules and the miRNAs were used to construct a ceRNA network. Next, the prognostic value of the constituents of the ceRNA network was evaluated by survival analysis. Furthermore, a risk score model for predicting progression-free survival (PFS) of NPC patients was established via lasso penalized Cox regression based on the differentially expressed genes, and the differences in the expression of the lncRNAs and mRNAs in the ceRNA network between high- and low-risk groups were investigated.Results: Fourteen stable modules were identified using GSE102349 based on WGCNA. A ceRNA network composed of 11 lncRNAs, 15 miRNAs and 40 mRNAs was established. The lncRNAs and mRNAs in this network were from turquoise and salmon modules. Survival analysis indicated that ZNF667-AS1, four mRNAs (LDHA, LMNB2, TPI1, and UNG), and hsa-miR-142-3p in the ceRNA network were significantly correlated with the prognosis of NPC. Gene set enrichment analysis indicated that the up-regulation of ZNF667-AS1 was associated with some immune-related pathways. Besides, a risk score model consisting of 12 genes was constructed and showed a good performance in predicting PFS in NPC patients. Among the 11 lncRNAs in the ceRNA network, SNHG16, SNHG17, and THAP9-AS1 were up-regulated in the high-risk group of NPC, while ZNF667-AS1 was down-regulated in the high-risk group of NPC.Conclusions: These results will promote our understanding of the crosstalk among lncRNAs, miRNAs, and mRNAs in the tumorigenesis and progression of NPC.