Background Tick-borne encephalitis (TBE) is a severe, vaccine-preventable viral infection of the central nervous system. Symptoms are generally milder in children and adolescents than in adults, though severe disease does occur. A better understanding of the disease burden and duration of vaccine-mediated protection is important for vaccination recommendations. Aim To estimate TBE vaccination coverage, disease severity and vaccine effectiveness (VE) among individuals aged 0–17 years in Switzerland. Methods Vaccination coverage between 2005 and 2022 was estimated using the Swiss National Vaccination Coverage Survey (SNVCS), a nationwide, repeated cross-sectional study assessing vaccine uptake. Incidence and severity of TBE between 2005 and 2022 were determined using data from the Swiss disease surveillance system and VE was calculated using a case–control analysis, matching TBE cases with SNVCS controls. Results Over the study period, vaccination coverage increased substantially, from 4.8% (95% confidence interval (CI): 4.1–5.5%) to 50.1% (95% CI: 48.3–52.0%). Reported clinical symptoms in TBE cases were similar irrespective of age. Neurological involvement was less likely in incompletely (1–2 doses) and completely (≥ 3 doses) vaccinated cases compared with unvaccinated ones. For incomplete vaccination, VE was 66.2% (95% CI: 42.3–80.2), whereas VE for complete vaccination was 90.8% (95% CI: 87.7–96.4). Vaccine effectiveness remained high, 83.9% (95% CI: 69.0–91.7) up to 10 years since last vaccination. Conclusions Even children younger than 5 years can experience severe TBE. Incomplete and complete vaccination protect against neurological manifestations of the disease. Complete vaccination offers durable protection up to 10 years against TBE.