The move was "based on a medical assessment for the individual," a defense official told AFP. "It was the right decision to make," said the official, who spoke on condition of anonymity.
Hormone therapy was approved recently by Colonel Erica Nelson, commandant of the US Disciplinary Barracks at Fort Leavenworth, Kansas, where Manning is now serving a 35-year prison sentence for his massive document dump, officials said.
"But the delay in treatment came with a significant cost to Chelsea and her mental health and we are hopeful that the government continues to meet Chelsea's medical needs as is its obligation under the Constitution so that those harms may be mitigated," it said.
Manning's lawsuit had argued that the Defense Department was violating her constitutional rights in refusing to grant hormone therapy, as the situation amounted to "cruel and unusual" punishment.
The former intelligence analyst also had been allowed to wear women's underwear following a decision last year, and to undergo psychotherapy.
Manning was convicted in August 2013 of espionage and other offenses after admitting to handing over more than 700,000 classified documents to the WikiLeaks website while stationed in Iraq.
