ENY2 (Enhancer of yellow 2 transcription factor) is a transcription nuclear protein and primarily participates in the course of mRNA export and histone deubiquitination to influence gene expression. Current studies have shown that the expression of ENY2 is significantly upregulated in multiple cancers. However, the exact association between ENY2 and pan-cancers has not been fully established. Here, we comprehensively analyzed ENY2 from the online public database and The Cancer Genome Atlas (TCGA) database, including gene expression level in pan-cancer, comparison of ENY2 expression in different molecular and immune subtypes of pan-cancer, targeted protein, biological functions, molecular signatures, diagnostic and prognostic value in pan-cancer. Moreover, we focused on head and neck squamous cell carcinoma (HNSC) and explored ENY2 from the perspective of the correlations with clinical characteristics, prognosis, co-expression genes, differentially expressed genes (DEGs) and immune Infiltration. Our findings showed that the expression of ENY2 differed enormously not only in most cancer types but also in different molecular and immune subtypes of cancers. High accuracy in predicting cancers and notable correlations with prognosis of certain cancers suggested that ENY2 might be a potential diagnostic and prognostic biomarker of cancers. In addition, ENY2 was identified to be significantly correlated with clinical stage, gender, histologic grade and lymphovascular invasion in HNSC. Overexpression of ENY2 could lead to a worse overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in HNSC, especially in different clinical subgroups of HNSC. Taken together, ENY2 showed strong correlation with the diagnosis and prognosis of pan-cancer, and was an independent prognostic risk factor of HNSC, which may serve as a potential target for cancer management.