Tick-borne encephalitis (TBE) is peculiar due to its unstable dynamics with profound inter-annual fluctuations in case numbers – a phenomenon not well understood to date. Possible reasons – apart from variable human contact with TBE foci – include external factors, e.g. climatic forcing, autonomous oscillations of the disease system itself, or a combined action of both. Spectral analysis of TBE data from six regions of central Europe (CE) revealed that the ostensibly chaotic dynamics can be explained in terms of four superposed (quasi-)periodical oscillations: a quasi-biennial, triennial, pentennial, and a decadal cycle. These oscillations exhibit a high degree of regularity and synchrony across CE. Nevertheless, some amplitude and phase variations are responsible for regional differences in incidence patterns. In addition, periodic changes occur in the degree of synchrony in the regions: marked in-phase periods alternate with rather off-phase periods. Such a feature in the disease dynamics implies that it arises as basically diverging self-oscillations of local disease systems which, at intervals, receive synchronizing impulses, such as periodic variations in food availability for key hosts driven by external factors. This makes the disease dynamics synchronized over a large area during peaks in the synchronization signal, shifting to asynchrony in the time in between.