Influenza vaccination is the main method of preventing influenza. Vaccination is recommended for certain individuals with diseases that could cause complications in the case of flu infection. The objective of this retrospective observational study was to examine influenza vaccination coverage in patients with risk factors, to describe the characteristics of those vaccinated and to study the influence of COVID-19. The study population was children under 14 years old with risk factors between 2018/19 and 2022/23 in Central Catalonia, sourced through the electronic database of the Catalan Institute of Health. The association of influenza vaccination data with sociodemographic data and risk factors was performed by bivariate and multivariate analysis. A total of 13,137 children were studied. Of those, 4623 had received the influenza vaccine in at least one season. The average influenza vaccination rate was 28.8%. The statistically significant factors associated with vaccination were age and having certain risk factors: asthma, diabetes, haemoglobinopathies and clotting disorders. In all seasons, the immigrant population was vaccinated more than the native population p < 0.05, except for the COVID-19 season (2020/21), where no differences were observed. Of those vaccinated, 7.1% had been vaccinated for 5 consecutive years. Influenza vaccination coverage in the paediatric age group was low. Vaccination promotion measures must be implemented. COVID-19 meant an increase in vaccination of the native population to the same level as that of the immigrant population.