NOTE: There may be an error on the exact burial section on some people. It is recommended that you stop by the Visitor's Building and double check the Kiosk before physically searching for a relative or friend. A layout map of the cemetery is available.

Fort Bliss itself was not established until the 1840s, but burials were made in the area of the cemetery as early as 1833. The fort was used as a Confederate infantry post during the Civil War, a cavalry post for training during World War I, and then became a demobilization camp after the war. Before Ft. Bliss was moved, soldiers were buried at what is now Cleveland Square and the downtown El Paso Public Library. Union soldiers buried there were removed and reburied at Fort Snelling in 1883. In 1893, this former Ft. Bliss cemetery was granted to the City of El Paso.

In 1894, the area where the cemetery is currently located was designated as the Fort Bliss Post Cemetery. In 1914, the cemetery measured just 2.2 acres (0.89 ha); an additional 2.2 acres were added during the war. In 1939, funds were allocated for improvements and plans were approved to designate it a national cemetery.

In addition to being the final resting place of American soldiers, Fort Bliss National Cemetery was chosen by the Chinese government as the place of interment for 52 Republic of China Air Force cadets who died while training at the fort in 1944. Several German prisoners of war, and three Japanese civilians who were transferred from a cemetery in Lordsburg, New Mexico were also interred here, as were a German scientist who died while participating in research projects at Fort Bliss during World War II and an officer of the British Royal Air Force who served during that same war.

In order to make way for new construction in the central business district in New Orleans, Louisiana in 1955, the remains of the Fort's namesake Lieutenant Colonel William Wallace Smith Bliss (1815–1853) were disinterred from Girod Street Cemetery in New Orleans and brought to Fort Bliss, along with the monument erected in his memory.

In June 1973, the Veterans Administration took over operational duties of the cemetery. During the 1990s, twenty acres were added to the cemetery which were given by the Department of the Army.

In 2002, the cemetery was using 90 million gallons of water a year to keep the grass in the area green. Plans for xeriscaping the cemetery began discussion in 2002.

The xeriscaping was opposed by many because it was felt that xeriscaping looked less dignified or respectful, according to the El Paso Times. In 2007, the cemetery was xeriscaped with a budget of $4.2 million to convert the land. William F. Tuerk, director of the National Cemetery Administration oversaw the change. In 2013, the cemetery won the Texas Environmental Excellence Award because it was saving an average of $400,000 a year because of cutting costs for water and grass upkeep.