Head and neck squamous cell carcinoma (HNSCC) ranks among the most prevalent malignancies with a poor prognosis. The underlying mechanisms driving HNSCC carcinogenesis are not fully elucidated. In this study, we identified dual specificity phosphatase 9 (DUSP9) as a carcinogenic factor in HNSCC development. According to the public data, DUSP9 was significantly up-regulated in HNSCC tumor tissues compared to normal tissues, confirmed by clinical data and single-cell RNA sequencing (scRNA-seq) data. Survival analysis revealed that high levels of DUSP9 expression contribute to poor prognosis in HNSCC patients. Knockdown of DUSP9 decreased, but overexpression of DUSP9 increased the proliferation and migration of HNSCC cells. ScRNA-seq data analysis suggested that DUSP9 was selectively expressed in tumor cells, with negligible expression in immune cells and stromal cells, and showed an elevated trend from primary tissues to metastatic tissues. Enrichment analyses of DUSP9-correlated genes suggested the involvement of DUSP9 in cell adhesion, wound healing, cell migration, transcription regulation and metabolic process. Furthermore, DUSP9 expression in tumor tissues exhibited an inverse relationship with immune cell infiltration within the tumor microenvironment (TME). In conclusion, this study provided evidence that DUSP9 was up-regulated in HNSCC tissues and may play a pivotal role in HNSCC progression, suggesting its potential as a novel biomarker.