Two autochthonous (locally acquired) cases of tick-borne encephalitis (TBE) were detected in the Netherlands in July 2016, shortly after awareness was raised that TBE virus had been found in ticks in the country. Both patients showed typical biphasic symptoms of TBE and tested positive for TBE virus antibodies and RNA. Genetic analysis found the virus in one patient was distinct from viruses previously found in Dutch ticks. This provides strong evidence that TBE is endemic in the Netherlands. Researchers recommend further studies to assess the spread and prevalence of TBE virus in ticks, deer, sheep and high-risk human groups in the country.