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The human leukocyte antigene E (HLA-E) is associated with tumorigenesis in various cancers. Immunoncology along with sex-specific aspects in cancer therapy are now in scientific focus. Therefore, immunohistochemical HLA-E expression was retrospectively analysed in a cohort of oral squamous cell carcinomas (OSCC) after surgical therapy. Then, serum concentration of HLA-E (sHLA-E) was quantified in a prospective cohort by enzyme-linked immunosorbent assay. High HLA-E expression was associated with advanced UICC stage (Spearman’s correlation: <i>p</i> = 0.002) and worse survival (Cox-regression: progression-free survival: hazard ratio (HR) 3.129, confidence range (CI) 1.443–6.787, <i>p</i> = 0.004; overall survival: HR 2.328, CI 1.071–5.060, <i>p</i> = 0.033). The sHLA-E concentration was significantly higher in the control group than in tumor group (Mann–Whitney U-test (MW-U): <i>p</i> = 0.021). Within the tumor group, women showed significantly higher sHLA-E levels than men (MW-U: <i>p</i> = 0.049). A closer look at the tumor group and the control group showed that gender-specific differences exist: while no differences in sHLA-E concentration were detectable between female subjects of tumor group and control group (MW-U: <i>p</i> = 0.916), male subjects of tumor group had a significantly lower sHLA-E concentration compared to those of control group (MW-U: <i>p</i> = 0.001). In summary, our results provide evidence for sex-specific differences in immune responses in OSCC. This fact should be considered regarding future immunotherapy regimens.