Oncogene mutations contribute to carcinogenesis and can provide potential therapeutic targets for clinical anticancer management. However, oncogene mutation patterns in nasopharyngeal carcinoma (NPC) have yet to be fully elucidated. To gain insight into mutation patterns in NPC, a high-throughput OncoCarta panel assay was used to determine 238 hotspot mutations across 19 common oncogenes in 8 NPC cell lines and 160 NPC patient samples from southern China. Statistical analyses were further conducted to identify associations between oncogene mutations and selected clinicopathological characteristics. In total, we identified 24 mutations across 11 oncogenes in 17 (10.6%) NPC patients. Four patients exhibited mutations in at least one oncogene. We also identified a PIK3CA H1047R mutant in 7 NPC cell lines. In addition, oncogene mutations showed no correlation with either risk habits (smoking and drinking) or other clinical characteristics except for TNM stage. KIT mutations were associated with poorer overall and relapse-free survival. Furthermore, KIT mutations together with age and N stage were independent prognostic factors in NPC. Taken together, the present study is the first report on mutations in multiple oncogenes in NPC. We found that hotspot oncogene mutations are infrequent in NPC patients from southern China. The lack of hotspot mutations requires a comprehensive characterization of gene mutations in NPC for developing new therapeutic targets in the future.