Background: Most of the studies included in this analysis highlighted miRNAsrole in the prognosis of nasopharyngeal carcinoma (NPC) patients. Our aim in this bioinformatics study was to synthesize relevant data associated with NPC to identify new prognostic markers. Methods: miRNA and mRNA data related to NPC were downloaded from the Gene Expression Omnibus (GEO) database. A variety of online analytical tools (starBase, TargetScanHuman7.2, Metascape, Cytoscape_v3.6.0, and GEPIA) were used to analyze the downloaded data to identify biomarkers with extremely high sensitivity and further research value. Results: Changes in the expression levels of 13 miRNAs played crucial roles in the overall survival of NPC patients (miR-375 was down-regulated, miR-96-5p, miR-155-5p, miR-320a, miR-378a-3p, miR-15b-5p, miR-21-5p, miR-25-3p, miR-93-5p, miR-493-3p, miR-493-5p, miR-494-3p, and let-7i-5p were up-regulated). Additionally, eight central genes (CDK1, CCNB1, CCNA2, TOP2A, AURKA, MAD2L1, CDC6, and CHEK1) were identified as target genes for further NPC therapy. Conclusions: Our findings further elucidate the underlying relationship between miRNAs and prognosis in NPC. The identified miRNAs are closely related to NPC prognosis and have extremely high research value for future medical treatment.