Abstract Background The prevalence of vaccination hesitancy has become one of the top ten global health problems. During the Covid-19 pandemic several studies reported negative correlation of vaccination hesitancy with fear of Covid-19 and anxiety. Therefore, the study aimed to explore how fear and anxiety can impact one’s intent to get vaccinated. Methods In 2021, data from 5999 post-secondary Slovenian students was gathered using a cross-sectional online survey. Binary logistic regression and the Sprearman correlation coefficient was used to explore the relation between Fear of Covid-19 Scale (FCOV), Generalized Anxiety Disorder Questionnaire (ANX) and a question regarding participants’ intentions to get vaccinated. Results Results showed that only 39.7% of students expressed intention to get vaccinated as soon as possible and 29.2% exhibited no intentions to do so. Logistic regression indicated that only FCOV had a mild and significant (p < 0.001) impact on students’ intentions to get vaccinated, whereas ANX was found to have only a weak significant (p < 0.01) effect on students’ intentions to do so. Similarly, ANOVA test showed significant differences with small to medium effect of FCOV on intentions to get vaccinated, but no significant differences were found for ANX. Conclusions A low percentage of Slovenian tertiary students expressed intentions to get vaccinated as soon as possible for Covid-19, with only fear having been found to have a small to mild effect on students’ intentions to do so. Anxiety, on the other hand, was found to have a small positively predictive effect on vaccination hesitancy, which could reflect affective forecasting error (i.e. believing that the negative consequences of getting vaccinated would be greater than they really are). Therefore, when considering strategies to address the increasing problem of vaccination hesitancy, one must keep in mind that the loss-framed messages might not be sufficient to prompt people to get vaccinated. Key messages • Fear of Covid-19 had only a small to medium significant positive effect on students’ expressed intentions to get vaccinated as soon as possible. • The loss-framed messages might not be sufficient to prompt people to get vaccinated.