Background: Health Literacy (HL) has been recently hypothesized to affect the relationship between socio-economic status (SES) and health conditions. However, to date no study has yet assessed the potential contribution of HL in the pathway through which SES affects influenza vaccination status. We aim to examine the relationships among HL, SES factors, and influenza vaccination uptake in Tuscan (Italy) residents belonging to different high-risk groups (HRGs) for influenza. Methods: The study was performed within the Tuscan population sample selected in the Italian Behavioral Risk Factor Surveillance System in 2017–2018. HL was assessed using the Italian version of the 6-items European Health Literacy Survey Questionnaire (HLS-EU-Q6). Mediation analyses were conducted using SES variables as independent variables, influenza vaccination status as dependent variable and HL as mediator variable. Results: A total of 3278 people belonged to HRGs for influenza. In the whole sample, 19.4% of the participants were vaccinated against influenza. Participants who were not employed or had a poor financial status were more likely to be vaccinated against influenza (OR 1.56, 95%CI 1.26–1.94, p < 0.001, and OR 1.21, 95%CI 1.00–1.48, p = 0.047 respectively). HL did not mediate the relationship of any of the independent variables with influenza vaccination status. Conclusions: Some SES determinants resulted to influence influenza vaccination uptake, while HL did not affect the likelihood of influenza vaccination uptake among HRGs. Universal health care systems, as in the case of Italy, offering influenza vaccination free of charge to HRGs help in reducing inequalities and mitigating HL demands.