<p>Epigenetic modifications act as crucial controllers of gene expression in nasopharyngeal carcinoma (NPC), with DNA hypermethylation of tumour suppressor genes and alterations in histone modification patterns playing a major role in oncogenesis. EBV-encoded proteins directly modulate host epigenetic machinery, promoting stable silencing of critical genes. Environmental exposures, such as nitrosamines and tobacco smoke, further influence epigenetic risk. Non-coding RNAs, especially miRNAs and lncRNAs, modulate epigenetic regulators and contribute to tumour behaviour. Several epigenetic markers show strong potential as non-invasive diagnostic and prognostic tools. Epigenetic drugs, such as HDAC and DNMT inhibitors, therapeutically show promise in reactivating silenced genes and sensitising tumours to conventional treatments. Epigenomic alterations offer profound insights into NPC pathogenesis and present valuable opportunities for early detection, risk assessment and targeted therapy. With the advances in epigenomic profiling technologies and increasing clinical validation, epigenetic biomarkers and therapeutics may become integral to precision oncology approaches in NPC. Continued interdisciplinary research is essential to fully harness these insights and translate them into improved outcomes for patients. This review presents an in-depth summary of the current understanding regarding epigenomic alterations in NPC, with a focus on their biological significance, diagnostic utility, and therapeutic potential in NPC initiation, progression and treatment.</p>