Speaking to CNN, he said he was afraid the South Korean military would find out he was talking to the media. He faces charges for having sexual relations with another man, a crime within the South Korean military punishable by up to two years in prison.
Sergeant A is part of a wider investigation which human rights groups are calling a homophobic witch-hunt, an accusation the military rejects.
Homosexuality is not illegal for civilians in South Korea but human rights groups say the rights of sexual minorities are not always protected.
Investigators visited Sergeant A in March -- telling him they knew he was gay and his ex-partner had already admitted their "crimes."
They asked him deeply personal and explicit questions, leaving him feeling "uncomfortable and humiliated," Sergeant A told CNN.
"The atmosphere was very oppressive and humiliating," he said. "I was scared."
The South Korea military and the defense ministry declined multiple requests for an interview and referred CNN to an April statement:
"To keep the military community sound and given the special nature of military discipline, sexual relations with same sex soldiers are being punished as 'disgraceful conduct' under military law."
The military penal code bans homosexual activity under Article 92-6 "to keep the military community sound."
The law regards same-sex relations between soldiers as "disgraceful conduct," akin to sexual assault. One man convicted last month was given a six month suspended prison sentence.
In a statement, Amnesty International East Asia director Roseann Rife called for the conviction to be immediately overturned and the group condemned what it described as "an outrageous military gay witch-hunt."
The recent investigation started earlier this year after a video was posted on social media showing two male soldiers having sex.
Since then, according to human rights groups and local media, at least 32 soldiers have been charged. The military declined to give a number.
Lim Tae-hoon, an activist with the Military Human Rights Center for Korea (MHRCK), said the military has been using gay dating apps to try and track down homosexual soldiers.
Sergeant A told CNN his phone was taken and its contents copied, he claimed investigators insinuated his unit would find out about his sexuality if he refused.
"They knew that I would not want my identity revealed so they made me cooperate in the investigation," he said.
Amnesty has called on Seoul to "repeal this archaic and discriminatory provision in the military criminal code," criticizing the government for being slow to protect the rights of sexual minorities within the country.
During the recent election campaign, now President Moon Jae-in drew intense criticism from LGBT groups after he said he was "opposed" to homosexuality in a televised debate.
Days later he walked that back slightly, saying that it was "still a little early to allow homosexuality within the military" on the ground that South Korean society was not ready for it. He has not broached the subject since being sworn in.