Fort Bayard bears the name of Brigadier General George Dashiell Bayard, who never saw the New Mexico highlands where his legacy would endure. Bayard fell mortally wounded at the Battle of Fredericksburg in December 1862, three and a half years before Company B of the 25th United States Colored Infantry Regiment established the remote outpost in his honor. A presidential order in 1869 set aside fifteen square miles as the Fort Bayard Military Reservation, creating federal land that would eventually include this sacred ground. The cemetery grew alongside the fort, receiving the remains of those who died defending settlers and miners along the Apache Trail.

The men who garrisoned Fort Bayard were among the most decorated African American soldiers of the frontier era. The 9th Cavalry Regiment patrolled these mountains and deserts, engaging Apache warriors in skirmishes that required extraordinary courage and endurance. Clinton Greaves earned his Medal of Honor here on January 24, 1877, for valor against Apache raiders. A young second lieutenant named John Pershing arrived in 1886 to install heliograph communications, launching a career that would make him commander of American forces in World War I. The monument to the Buffalo Soldiers that stands on the old parade field, erected in 1992, reminds visitors that these grounds witnessed some of the most significant chapters in African American military history.

When Geronimo surrendered in 1886, the Apache threat ended and Fort Bayard faced closure. Its salvation came from an unexpected source: U.S. Army Surgeon General George Miller Sternberg, who recognized that the fort's remarkable health records pointed to the therapeutic benefits of its high-altitude climate. Fort Bayard became the Army's first tuberculosis hospital in 1900. In 1922, when the facility transferred to the Veterans Administration, the cemetery officially became Fort Bayard National Cemetery. German prisoners of war were held at the partially reactivated fort during World War II, from 1943 to 1945. The cemetery joined the National Cemetery system in 1973, and New Mexico donated additional acreage in the 1990s.

Fort Bayard National Cemetery was placed on the National Register of Historic Places on July 7, 2002, as part of the broader Fort Bayard Historic District. Administered by Santa Fe National Cemetery, it continues to accept burials for eligible veterans and their families. The headstones tell stories spanning over a century and a half: Indian Wars veterans, tuberculosis patients who sought healing in the mountain air, soldiers from two World Wars, and servicemembers from every conflict since. The cemetery remains one of the only surviving 19th-century elements of the original fort, a place where the American military experience in the Southwest finds its most solemn expression among the juniper and pinyon of the high desert.