Tick-borne encephalitis (TBE) is a zoonotic disease causing meningitis, encephalitis, and meningoencephalitis. Tick-borne encephalitis virus (TBEV) is an etiological agent of TBE. From an analysis of five distinct sequences of Japanese TBEV, it has been proposed that Japanese TBEV was transmitted from Russia to Japan on just a single occasion 260–430 years ago. Here thirteen distinct nucleotide sequences encoding the entire region of the envelope protein for Japanese TBEV were analyzed. It is shown, from the phylogenetic analysis, that Japanese TBEV belongs to the Far Eastern subtype, which is known to be highly pathogenic. Japanese TBEV was divided into three groups, and TBEV was inferred to have been transmitted between Japan and Russia at least three times, which were estimated to have occurred several hundred years ago. These results indicate that TBEV has not only been endemic but also transmitted multiple times to Japan.