Despite its effectiveness in the prevention of seasonal flu, influenza vaccination uptake remains low, even among healthcare workers (HCWs), despite their occupational risk. The aim of this study was to explore the association between main reasons for accepting or refusing influenza vaccination and the decision to receive the vaccination during both previous and following year among health sciences students. A multi-center, cross-sectional study was performed using a validated online questionnaire. Data were analyzed by performing univariable and multivariable logistic analysis. Data from over 3000 participants showed that avoiding the spread of infection to family members and the general population (aOR: 43.55), as well as to patients (aOR: 16.56) were the main reasons associated with the highest probability of taking the influenza vaccination the following year. On the contrary, not considering influenza as a severe disease was the reason associated with the lowest probability for past (aOR: 0.17) and future vaccination (aOR: 0.01). Therefore, the importance of vaccination to protect others should always be the core of vaccination campaigns for health sciences students, together with tools to increase their awareness of the severity of this disease.