Two paediatric tick-borne encephalitis vaccines, Encepur Children and FSME-IMMUN Junior, are used widely in Europe. This study compared the immunogenicity and safety of both vaccines, administered using the conventional (Days 0, 28, and 300) or accelerated (Days 0, 14, and 300) schedule and evaluated whether a third dose of Encepur Children can complete a primary vaccination course initiated with FSME-IMMUN Junior. A total of 334 children 1 to < 11 years of age were enrolled in this Phase IV randomized, controlled, single-blind, multi-centre trial. All subjects, irrespective of study arm, received Encepur Children as the third dose on Day 300. The percentage of subjects with antibody titres > or = 10, as determined by neutralization test (NT), was assessed and local and systemic reactions were monitored and solicited. Within both the conventional and accelerated schedules, the proportion of subjects achieving an NT > or = 10 was higher in the group that received Encepur Children, compared with the group that received FSME-IMMUN Junior, at Days 42 and 300 (conventional schedule Day 300, P < 0.001 Encepur Children versus FSME-IMMUN Junior; accelerated schedule Days 42 and 300, P<0.001 Encepur Children versus FSME-IMMUN Junior). The third dose of Encepur Children led to a substantial increase in the proportion of subjects in the FSME-IMMUN Junior groups achieving NT > or = 10. Overall, >95% of all children achieved NT > or = 10, on completion of the primary vaccination course. Encepur Children provides an immune response, measured by neutralizing TBE antibodies, that is superior to FSME-IMMUN Junior and can successfully be used to complete a primary vaccination course initiated with FSME-IMMUN Junior. Both vaccines were well tolerated, with comparable safety profiles; no vaccine-related serious adverse events were reported.