Manning, who formerly went by the name Bradley Manning, was convicted of multiple counts of espionage for leaking more than 700,000 wartime documents and diplomatic cables to WikiLeaks, in a move that sparked debates about the Obama administration's prosecution of whistle-blowers.
In the suit, the American Civil Liberties Union contends that Army medical personnel diagnosed Manning with gender dysphoria in 2010, an identity disorder where a person rejects the gender they were assigned with at birth.
Manning is suing to receive hormone therapy, permission to follow female grooming standards and access to a doctor trained to deal with her condition.
"The government continues to deny Ms. Manning's access to necessary medical treatment for gender dysphoria, without which she will continue to suffer severe psychological harms," Chase Strangio, an attorney with the ACLU Gay Lesbian Bisexual and Transgender project, said in a statement. "Such clear disregard of well-established medical protocols constitutes cruel and unusual punishment."
Calls to the Department of Defense seeking comment were not immediately returned.
The suit contends the Army has taken little to no action in response to several requests from Manning to be treated as a female and to receive proper treatment for gender dysphoria.
Manning had previously petitioned to be transferred to a civilian prison facility, but Defense Secretary
Manning is also trying to obtain appropriate psychological therapy, according to the lawsuit. The only psychologist made available to Manning has admitted in written statements that she is not qualified to treat gender dysphoria, according to the court papers.
In an interview with the Los Angeles Times, Strangio said the military's response to Manning's requests for aid have been virtually non-existent.
Manning was provided with female undergarments, but has received little to no additional aid that would allow her to identify as female.
"What they've done alone is essentially no treatment at all and the constitution simply cannot stand for that," Strangio told The Times.
The lawsuit will not seek to have Manning transferred to a civilian prison, according to Strangio.
The documents and videos leaked by Manning revealed several acts of gross negligence by U.S. soldiers, including a helicopter attack in Baghdad that killed two journalists and several children.
However, defense officials have also argued that many of the documents Manning released endangered the lives of covert operatives and strained diplomatic relations by releasing privileged conversations where administration officials made derisive remarks about foreign allies.
Manning, who was sentenced to 35 years in prison, could become eligible for parole in 2021.