Geraldine Roman, 50, who became the Catholic-majority nation's first transgender person elected to Congress in 2016, took her oath on Wednesday.
"That indeed makes her the first transgender officer in the Armed Forces of the Philippines," defence department spokesman Arsenio Andolong said in a statement.
"Her being part of the (military) underscores the fact that gender is not an issue when it comes to serving the country," he added.
The Philippine military frequently inducts prominent figures like legislators and cabinet members as reserve officers.
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Roman was appointed as a lieutenant colonel in the army reserves, alongside two fellow House of Representatives members, the statement added.
"War and disaster do not recognise gender, it affects everybody, and everyone must defend and serve our communities, and our country," the statement quoted her saying during the ceremony.
Born to a politically prominent family based near Manila, Roman changed her gender in the 1990s.
Her political success has been hailed by lesbian, gay, bisexual and transgender (LGBT) campaigners in a conservative society where divorce and same-sex marriage are both banned.
The Philippine military last year announced it would accept LGBT applicants "as long as they act and move with dignity".
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