Manning's gender-identity struggle — a sense of being a woman in a man's body — was brought up by the defense at the court-martial, and a photo of the soldier in a blond wig and lipstick was submitted as evidence.
But the latest twist, announced Thursday, surprised many and confronted the Pentagon with questions about where and how the Army private is to be imprisoned.
The former Army intelligence analyst disclosed the decision in a statement provided to NBC's "Today" show.
"As I transition into this next phase of my life, I want everyone to know the real me. I am Chelsea Manning. I am a female. Given the way that I feel, and have felt since childhood, I want to begin hormone therapy as soon as possible," the statement read.
The statement asked people to use the feminine pronoun when referring to Manning. It was signed "Chelsea E.Manning" and included a handwritten signature.
The soldier's attorney, David Coombs, told "Today" he hopes officials at the military prison at Fort Leavenworth, Kan., accommodate Manning's request for hormone treatment, which typically involves high doses of estrogen to promote breast development and other female characteristics.
However, George Wright, an Army spokesman at the Pentagon, said the Army does not provide such treatment or sex-reassignment surgery. He said soldiers behind bars are given access to psychiatrists and other mental health professionals.
A lawsuit could be in the offing. Coombs said he will do "everything in my power" to make sure Manning gets his way. And the American Civil Liberties Union, the Human Rights Campaign and other advocates for gays, bisexuals and transgender people said Manning deserves the treatment.
"In the United States, it is illegal to deny health care to prisoners. That is fairly settled law," said Mara Keisling, executive director of the National Center for Transgender Equality. "Now the Army can claim this isn't health care, but they have the weight of the medical profession and science against them."
With Manning in custody and unavailable to comment, the AP is seeking additional information about the statement from Coombs, who did not immediately respond to email and telephone messages. For the time being, AP stories will use gender neutral references to Manning and provide the pertinent background on the transgender issue.
A Federal Bureau of Prisons policy implemented last year requires federal prisons to develop treatment plans, including hormone treatment if necessary, for inmates diagnosed with gender-identity disorder. But the bureau oversees only civilian prisons.
Manning's case appeared to be the first time the therapy had come up for a military prisoner.
Manning, 25, was convicted of Espionage Act violations and other crimes for turning more than 700,000 classified military and diplomatic documents over to the secrets-spilling website WikiLeaks. Coombs said the soldier could be paroled from prison in as little as seven years.
After sentencing, Manning was returned Thursday to Fort Leavenworth.
Fort Leavenworth is an all-male prison. But the staff has some leeway to separate soldiers from the other inmates based on the risk to themselves and others, prison spokesman George Marcec said.
Manning would not be allowed to wear a wig or bra, and would have to meet the military standard for hair, Marcec said. In addition, Marcec said if Manning wants to go by Chelsea in the prison, a name change would have to be approved in court and then a petition submitted with the Army to change its records.
Advocates said gays and transgender people are more susceptible to sexual assault and other violence in prison.
"She most likely will need to be placed with a female prison population because she identifies as female," said Jeffrey Parsons, a psychology professor at Hunter College in New York.
Under a special agreement, the Army sends its female prisoners to a Navy women's jail in Miramar, Calif. It also has an agreement under which it can send soldiers to federal civilian prisons.
Greg Rinckey, a former Army prosecutor and now a lawyer in Albany, N.Y., said Manning's statement could be a ploy to get transferred to a civilian prison.
"He might be angling to go there because he believes life at a federal prison could be easier than life at the disciplinary barracks at Fort Leavenworth," Rinckey said.
He also said the military is adamant about not providing hormone treatment: "You enlisted as a male, you're a male, you're going to be incarcerated as a male."
Associated Press writers Lauran Neergaard and Sagar Meghani in Washington and John Milburn in Topeka, Kan., contributed to this report.