[3] January 3, 1919, the date when Japan recognized Lithuania de facto[4] is considered the beginning of the bilateral relations.

In 1940, Chiune Sugihara assisted the flight of Jewish refugees from the imminent Nazi invasion of Lithuania by issuing them transit visas from the consulate in Kaunas, despite instructions from the Japanese Government attempting to block his actions.

[7] Japan de facto re-recognized Lithuania on September 6, 1991, and a month later diplomatic relations were re-established between these countries.

Minister of Foreign Affairs of Lithuania Linas Antanas Linkevičius welcomed the Japanese vessels and their steadfast partnership based on the same fundamental values since 1991 as well as referred an honorable and righteous diplomat Chiune Sugihara,[10] who served as the Japanese Vice-Consul at Kaunas from 1939 to 1940 and granted visas to thousands of Jewish and other minority refugees in his short term of office.

[12] In April 2001, Lithuanian President Valdas Adamkus paid an official visit to Japan, and on April 11, he held talks with Japanese Prime Minister Yoshiro Mori about their views on several issues that includes their bilateral relations, Japan–Russia relations and Lithuania's accession to EU and NATO.