From another article:
Leavenworth is an all-male prison. Spokesman George Marcec said there had never been a case similar to Manning's, and the soldier would need to petition for a transfer to a federal prison to receive hormone treatment.
Courthouse News has more on the case law regarding prison obligations to provide hormone therapy.
Here are the current DoD Directive Administration of Military Correctional Facilities and Clemency and Parole Authority on military prisons. There are procedures for transfer from a military prison to a federal prison. BOP's program directive is here.
The most recent BOP program directive I found on transgender medical care is 6031.03, Patient Care, 8/23/12. It replaces 6031.01 from 2005. It describes the change as "Clarifies the assessment and treatment of inmates with the possible diagnosis of Gender Identity Disorder (GID)." On page 37:
If a diagnosis of GID is reached, a proposed treatment plan will be developed which promotes the physical and mental stability of the patient. The development of the treatment plan is not solely dependent on services provided or the inmate’s life experiences prior to incarceration. The treatment plan may include elements or services that were, or were not, provided prior to incarceration, including, but not limited to: those elements of the real life experience consistent with the prison environment, hormone therapy, and counseling. Treatment plans will be reviewed regularly and updated as necessary.
Current, accepted standards of care will be used as a reference for developing the treatment plan. All appropriate treatment options prescribed for inmates with GID in currently accepted standards of care will be taken into consideration during evaluation by the appropriate medical and mental health care staff. Each treatment plan or denial of treatment must be reviewed by the Medical Director or BOP Chief Psychiatrist. Hormone therapy must be requested through the non-formulary review process, and approved by the Medical Director and /or Chief Psychiatrist. Consultation with the Chief of Psychology prior to such approval may be appropriate in some cases.
In summary, inmates in the custody of the Bureau with a possible diagnosis of GID will receive a current individualized assessment and evaluation. Treatment options will not be precluded solely due to level of services received, or lack of services, prior to incarceration.
In 2012, Denver revised its jail policy for transgender inmates. (Article here.)
Last month, the Palm Center announced grants totaling 1.35 million from the Tawani Foundation and Wells Fargo for a multiyear initiative to study transgender service in the U.S. military.
DoD Issuances and Directives are here.