[1] She was the daughter of Kusumoto Taki, who was a courtesan from Nagasaki; and the German physician Philipp Franz von Siebold, who worked on Dejima, an island foreigners were restricted to during Japan's long period of seclusion from the world.

[d][7] Ine lived with her parents on Dejima until Siebold was banished[5] on 22 October 1829[8] for allegedly exporting restricted information illicitly gathered from the geographer Takahashi Kageyasu [ja].

[8] Taki and the two-year-old Ine were not permitted to leave Japan;[e][5] they waved him goodbye from a small boat in the harbour as his ship left.

He sent Ine books of Dutch grammar, important for Western studies at the time in Japan, and students of Siebold's contributed to her education.

An apocryphal story tells of Ine running away at age 14 or 15 to study medicine with one of them, Ninomiya Keisaku [ja], in Uwajima Domain,[5] where he had been placed under house arrest for his involvement in the Siebold Affair.

[9] Ine's medical training got an official start in 1845 when she began studying obstetrics in Okayama Domain under another of Siebold's students, Ishii Sōken [ja],[g][10] through the introduction of Ninomiya Keisaku.

[12] Japan's seclusion came to an end in 1854 and in 1859 Nagasaki was opened as a treaty port and the Dutch abandoned Dejima for a consulate in the capital city Edo (modern Tokyo).

[1] Ine continued to learn from Dutch physicians in the Nagasaki community such as J. L. C. Pompe van Meerdervoort, who lauded her skills in print.

Van Meerdervoort founded in 1861 the first Western-style hospital and medical school in Japan, the Nagasaki Yōjōsho, with the support of the military government, and Ine attended classes in the women's ward and assisted in operations there.

[16] Her reputation and connections in the Western-learning community won Ine the patronage of Date Munenari, whose favour extended to her daughter, now named Takako.

[j][4] He extended a modest official rice stipend to Ine, and she was expected to be ready to serve in the women's quarters at the castle; she was one of three doctors present when Munenari's wife Yoshiko gave birth in 1867.

About this time Ine studied obstetrics in Nagasaki with Antonius Bauduin, who pioneered ovariotomy there and was appointed to the Tōkō national medical school in Tokyo, which had just been renamed from Edo and where the Emperor had moved after his restoration.

[25] A volume written by Keiko Hamada [ja] and illustrated by Takashi Yorimitsu [ja] titled Nihon de Hajimete no Joi: Kusumoto Ine ("The First Woman Doctor in Japan: Kusumoto Ine")[n] appeared in 1992 as part of the Denki: Ningen ni Manabō ("Biography: Learn from People")[o] series of biographies for youths.