The cause of death of Byun Hee-soo, a transgender rights campaigner, is not yet known.
She launched a landmark legal challenge against the military in January last year over her dismissal.
Her petition for reinstatement was rejected in July.
South Korea remains conservative on matters of sexual identity.
The 23-year-old had been receiving counselling from a mental health centre in her home province of Gyeonggi, north of Seoul. Her counsellor became concerned after not hearing from her since 28 February and called emergency services.
Ms Byun's case triggered debate about the treatment of transgender troops and soldiers from the LGBTQ community in the country.
She previously told reporters that apart from her gender identity, she wanted to show everyone that she could also be one of the great soldiers who protect the country.
All able-bodied South Korean men are required to carry out military service for nearly two years.
In December, the National Human Rights Commission of Korea said the decision not to allow her to continue to serve in the military had no legal grounds. SOURCE: BBC
