Abstract Background The European-wide statistics show that the use of flu vaccination remains low and the differences between countries are significant, as are those between different population groups within each country. Considerable research has focused on explaining vaccination uptake in relation to socio-economic and demographic characteristics, health promotion and health behavior factors. Nevertheless, few studies have aimed to analyze between-country differences in the use of flu vaccination for the EU population. To address this gap, this study examines the socio-economic inequalities in the use of influenza vaccination for the population aged 15 years and over in all 27 EU Member States and two other non-EU countries (Iceland and Norway). Methods Using data from the third wave of European Health Interview Survey (EHIS) 2019, we employed a multilevel logistic model with a random intercept for country, which allows controlling simultaneously the variations in individuals’ characteristics and macro-contextual factors which could influence the use of flu vaccination. In addition, the analysis considers the population stratified into four age groups, namely adolescents, young adults, adults and elderly, to better capture heterogeneities in flu vaccination uptake. Results The main findings confirm the existence of socio-economic inequalities between individuals in different age groups, but also of significant variation between European countries, particularly for older people, in the use of influenza vaccination. In this respect, income and education are strong proxy of socio-economic status associated with flu vaccination uptake. Moreover, these disparities within each population group are also explained by area of residence and occupational status. Particularly for the elderly, the differences between individuals in vaccine utilization are also explained by country-level factors, such as the type of healthcare system adopted in each country, public funding, personal health expenditure burden, or the availability of generalist practitioners. Conclusions Overall, our findings reveal that vaccination against seasonal influenza remains a critical public health intervention and bring attention to the relevance of conceiving and implementing context-specific strategies to ensure equitable access to vaccines for all EU citizens.