TBE vaccination strategies capable of inducing strong paediatric immunogenicity and acceptable reactogenicity are still under evaluation. This single-blind, multi-center, randomized, controlled, phase III clinical study compared the immunogenicity and safety of the two paediatric TBE vaccines available in Europe (FSME-IMMUN Junior and Encepur Children) following administration of two doses of either vaccine in 303 children aged 1-11 years. Regardless of immunological test or viral antigen used, immunological responses were consistently higher in children vaccinated with FSME-IMMUN Junior than those vaccinated with Encepur Children. FSME-IMMUN Junior is also non-inferior to Encepur Children, with respect to NT seropositivity rates (p<0.0001). Systemic reaction rates were low and similar between the vaccines. However, among children aged 7-11 years, local reactions were significantly higher after the first (p<0.01) and second (p<0.001) vaccination with Encepur Children than with FSME-IMMUN Junior, affecting half the children in the former group: 22.4% and 10.2% with FSME-IMMUN Junior vs. 49.0% and 51.0% for Encepur Children.