Minamidaitōjima and Kitadaitōjima were possibly again sighted by the Spanish on 28 July 1587, by Pedro de Unamuno who named them the "Useless Islands" (Islas sin Provecho).

In 1900, a team of pioneers from Hachijōjima, one of the Izu Islands located 287 kilometres (178 mi) south of Tokyo led by Tamaoki Han'emon (1838 – 1910), became the first human inhabitants of the island, and started the cultivation of sugar cane.

During this period until World War II, Minamidaitōjima was owned in its entirety by Dai Nippon Sugar (now Dai Nippon Meiji Sugar), which provided community services and subsidized pricing for its employees, and of whom were seasonal workers from Okinawa and Taiwan.

As the war situation worsened for Japan, many of the civilian inhabitants were evacuated to Okinawa, Kyushu or Hachijojima in 1944.

The island was repeatedly bombed and shelled by the United States Navy from February to June 1945.

After World War II, the island was occupied by the United States, at which time its civilian population was 1426.