We reviewed tick-borne encephalitis (TBE) surveillance and epidemiology in Germany, as these underlie public health recommendations, foremost vaccination. We performed descriptive analyses of notification data (2001–2018, n = 6063) according to region, demographics and clinical manifestations and calculated incidence trends using negative binomial regression. Risk areas were defined based on incidence in administrative districts. Most cases (89%) occurred in the federal states of Baden-Wurttemberg and Bavaria, where annual TBE incidence fluctuated markedly between 0.7–2.0 cases/100,000 inhabitants. A slight but significantly increasing temporal trend was observed from 2001–2018 (age-adjusted incidence rate ratio (IRR) 1.02 (95% confidence interval (CI): 1.01–1.04)), primarily driven by high case numbers in 2017–2018. Mean incidence was highest in 40–69-year-olds and in males. More males (23.7%) than females (18.0%, p = 0.02) had severe disease (encephalitis or myelitis), which increased with age, as did case-fatality (0.4% overall; 2.1% among ≥70-year-olds). Risk areas increased from 129 districts in 2007 to 161 in 2019. Expansion occurred mainly within existent southern endemic areas, with slower contiguous north-eastern and patchy north-western spread. Median vaccination coverage at school entry in risk areas in 2016–2017 ranged from 20%–41% in 4 states. Increasing TBE vaccine uptake is an urgent priority, particularly in high-incidence risk areas.