The US Army soldier was convicted by court-martial in July 2013 of violations of the Espionage Act and other offenses, after disclosing to WikiLeaks nearly three-quarters of a million classified or unclassified but sensitive military and diplomatic documents.
Psychologists recommended in April that Chelsea Manning should receive the treatment.
The move comes after the US military in July lifted a ban on transgender people in the armed forces.
“I am unendingly relieved that the military is finally doing the right thing. I applaud them for that. This is all that I wanted – for them to let me be me,” Chelsea Manning, 28, said in a statement.
The US Army has so far declined to comment.
The American Civil Liberties Union (ACLU), which represented Chelsea Manning, confirmed that she would be provided with medical treatment.
ACLU lawyer Chase Strangio, said: “This is a monumental day for Chelsea, who can now enjoy some peace knowing that critically needed medical care is forthcoming.
“Thankfully the government has recognized its constitutional obligation to provide Chelsea with the medical care that she needs.”
Chelsea Manning began her hunger strike on September 9, saying she was being bullied by the US government and denied treatment for gender dysphoria.
In July, Chelsea Manning attempted suicide over the lack of treatment.
She will now be treated under the US military’s new transgender policy, which also allows troops to transition gender while serving and aims to set standards for medical care.
However Chelsea Manning’s campaign team said she could still face being put in solitary confinement as punishment for having tried to commit suicide.
Chelsea Manning, who was arrested as Bradley Manning, is serving a 35-year sentence at the all-male Fort Leavenworth military facility in Kansas.
She was convicted in a military court of leaking more than 700,000 secret files to WikiLeaks after having worked as an intelligence analyst in Iraq.
Shortly afterwards she announced Chelsea Manning would start living as a woman.
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