Risa Takenouchi, 26, entered the academy in the western region of Hiroshima along with about 20 men, after the Japan Maritime Self-Defense Force overturned previous restrictions.
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"I hope not to put too much pressure on myself as the first woman," she told reporters.
"Instead I hope to work with my classmates and train to become a submarine crew member."
The navy has long only allowed men to serve on submarines, citing the difficulty of accommodating gender privacy concerns.
But it changed the rules in late 2018, after assessing that gender-specific privacy needs can be met without major submarine remodelling, a navy spokesman told AFP.
"This is a part of our efforts for efficient use of human resources," he added.
Sisters in arms: Pakistan Army honours women serving in armed forces
Japan's military as a whole is attempting to expand the role of women in its ranks as the Self Defense Forces struggle to attract young talent, with local media saying the navy has had particular difficulty attracting candidates to serve on submarines.
Japanese Prime Minister Shinzo Abe has long advocated for expanding the role of women in the workplace, but the country remains stubbornly low in international gender rankings.
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