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Background: Seasonal influenza vaccination (SIV) of health care workers (HCWs) is critical in protecting patients’ and HCWs’ health. Our objective was to examine HCW SIV coverage and related determinants. Methods and Materials: A nationwide cross-sectional questionnaire survey was conducted among HCWs during the first half of 2021. The questionnaire (online or paper-based) included knowledge, attitude and practice questions regarding SIV, COVID-19 vaccines and vaccination. Results: Out of 6500 questionnaires administered, 2592 were completed (response rate: 39.9%). SIV coverage reached 69.4% (95% CI: 67.6–71.2%) based on self-reported vaccine uptake. Nurses and administrative staff were found to be more skeptical and have lower vaccine acceptance in comparison with physicians (aOR = 0.66 and aQR = 0.59, respectively). Other SIV hesitancy risk factors included working in secondary health care (aOR = 0.59) and working in northern Greece (aQR = 0.66). Determinants for SIV acceptance included being or living with high-risk people due to medical history (aOR = 1.84 and aOR = 1.46, respectively), positive attitudes towards routine vaccinations (aOR: 1.86), knowledge about COVID-19 vaccines (aOR = 1.53) and COVID-19 vaccine uptake (aOR = 3.45). The primary reason for SIV refusal was low risk perception (58.7%). Conclusions: SIV coverage (2020/2021) was relatively high, but remained far from formal recommendations. Specific occupational groups were skeptical and low-risk perception was the main reason for vaccine refusal. Targeted policies should be developed and enforced.