January 3, 1919, the date when Japan recognized Lithuania de facto is considered the beginning of the bilateral relations. On February 8, 1929 the agreement by which visas were abolished was signed between Japan and Lithuania, while in 1930 the Trade and shipping agreement was signed. On November 23, 1939 Japanese consulate was established, led by Vice Consul Chiune Sugihara. However, due to the occupation, the consulate was shut the following year.
During World War II, in 1940 a Japanese diplomat named Chiune Sugihara assisted the flight of Jewish refugees by issuing them transit visas in Kaunas, Lithuania. Sugihara was then a vice-consul at Japan's diplomatic mission had ignored instructions from the Japanese Government by issuing transit permits to Japan for Jewish families fleeing from Poland in the wake of the Nazi invasion. Up to 10,000 refugees were saved from this action.
There is a significant close partnership between the city of Kuji and Klaipėda, established in 1989.
Japan recognized Lithuania on September 6, 1991 and a month later diplomatic relations were re-established between these countries. In 1997 the Embassy of Japan was established in Vilnius and in 1998 the Embassy of Lithuania was established in Tokyo.
In 2007 Their Majesties the Emperor and Empress of Japan Akihito and Michiko paid an official visit to Lithuania.