During the Civil War, Pensacola was hotly contested, as it was considered to be the best port for access to the Gulf of Mexico.

Numerous soldiers on both sides were interred in the cemetery after falling in combat, or dying in nearby hospitals.

In each year, 1944, 1950, 1986, and 1990, more area was transferred from NAS Pensacola to expand the facilities for the cemetery.

Barrancas National Cemetery has a monument honoring those soldiers who died from yellow fever.

The cemetery also holds 17 casualties of the Second Seminole War and 10 British aviators (six Royal Navy, four Royal Air Force) killed during training at the Naval Air Station during World War II.