Greece and Japan established diplomatic relations in 1899, as both countries concluded a Treaty of Friendship, Commerce and Navigation.

The consulate closed during World War II (1935–45), Greece joined the Allies, while Japan the Axis.

In 1-3.05.03, the Japanese Prime Minister, Junichiro Koizumi, visited Greece for the EU-Japan summit during the Greek Presidency of the EU.

In 2000, the Greek-Japanese Chamber of Commerce was established as a non-profit organization, as the successful progress of the Association of Hellenic Japanese Business Co-operation.

The Greek-Japanese Chamber is aiming towards promoting mutual economic, commercial and business relations between Greece and Japan.

In 1999 celebratory cultural events were organized on both sides to mark the centenary of the establishment of diplomatic relations between Greece and Japan.

In 1922, during the Burning of Smyrna the Japanese freighter Tokei Maru saved many Greek refugees who were trying to escape from the Turks.

"[10] Lafcadio Hearn was a Greek-Irish-Japanese writer, translator, and teacher who introduced the culture and literature of Japan to the West.