Nasopharyngeal carcinoma (NPC) is a malignancy of the epithelial lining of the nasopharynx, characterized by a complex interplay between genetic predispositions, viral infections—particularly Epstein–Barr virus (EBV)—and epigenetic dysregulation. Recent advances have illuminated the pivotal role of epigenetic alterations, including DNA methylation, histone modification, and non-coding RNA-mediated regulation, in tumor initiation, progression, and therapy resistance. Aberrant promoter hypermethylation silences key tumor suppressor genes, while histone acetylation imbalance and chromatin remodeling anomalies promote oncogenic transcriptional programs. In addition, dysregulated microRNAs and long non-coding RNAs contribute to altered gene expression networks that exacerbate NPC pathogenesis. This review integrates current evidence from 2021 to 2025, emphasizing how epigenetic mechanisms intersect with viral oncogenesis, immune evasion, and tumor microenvironmental remodeling. Finally, emerging diagnostic biomarkers and novel epigenetic therapies—such as DNA methyltransferase inhibitors, histone deacetylase inhibitors, and CRISPR-based epigenome editing—are discussed as promising avenues for improved patient management in NPC.