It is operated by the Federal Bureau of Prisons, a division of the United States Department of Justice.

[3] Operations began in 1988 when the Bureau of Prisons negotiated a partnership with the United States Navy to lease land and several excess buildings at Saufley Field in exchange for inmate labor.

In 2006, the Bureau of Prisons decided to cut costs by closing the Federal Prison Camp, Eglin, which was located at Eglin Air Force Base, in Okaloosa County, Florida, and moving the inmates to FPC Pensacola.

[5] In October 2006 the United States Department of Justice indicted four people for bribery and providing contraband to inmates at the prison.

[6] In March 2007, the prison made headlines when an inmate escaped from a work detail at Naval Air Station Pensacola.