European hedgehogs (Erinaceus europaeus) have a high exposure to various ticks, which could transmit pathogens with direct health significance for the host and may have zoonotic potential. Tick-borne meningoencephalitis (FSME) is an important tick-borne disease in Switzerland, caused by the tick-borne encephalitis virus. About its occurrence in the European hedgehog population is little known. The present study examined various organs, blood and ticks of 65 European hedgehogs to obtain data of FSME virus presence in this species in Switzerland. Real-time RT-PCR from the lungs, liver, spleen and kidney of 56 hedgehogs and of 114 infesting ticks (Ixodes hexagonus or Ixodes ricinus) were used for the detection of viral RNA. In addition, 19 blood samples were tested for antibodies against FSME by ELISA. FSME virus antibodies were detected for the first time in the serum of a European hedgehog. Lung and spleen tissue samples of the same animal tested also weak virus positive on RT-PCR. Clinically, the hedgehog showed neurological symptoms, although these symptoms could have originated from an other diseases. No viral RNA was detected in any of the ticks. This study could not confirm if the meningoencephalitis in the hedgehog was triggered by the FSME viral infection. Nevertheless, the simultaneous detection of antibodies and virus RNA in the same animal makes the European hedgehog a competent host of the tick-borne encephalitis virus and leads to the assumption that this species can act as a reservoir.