Large-scale Japanese migration to Indonesia dates back to the late 19th century, though there was limited trade contact between Japan and Indonesia as early as the 17th century. As of October 2009, there were about 11,263 Japanese expatriates in Indonesia. At the same time, there are also identifiable populations of descendants of early migrants, who may be referred to as Nikkei Indonesians or Indonesian Nikkei.

Karayuki-san (唐行きさん) was the name given to Japanese girls and women in the late 19th and early 20th centuries who were trafficked from poverty-stricken agricultural prefectures in Japan to destinations in East Asia, Southeast Asia, Siberia, Manchuria, British India, and Australia, to serve as sex workers.