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Fort Bayard is located in southwestern New Mexico adjacent to the Gila National Forest. The site was chosen in 1863 for its springs and commanding view of the Apache war trails surrounding the nearby mining camps. In 1866, a permanent post was established here with the primary responsibility for protecting the Pinos Altos gold camp. The post was named Fort Bayard in honor of General G.D. Bayard, who died from wounds received during the Battle of Fredericksburg, and who had served in New Mexico and Arizona prior to the Civil War. The U.S. Army launched numerous attacks against the Apache from Fort Bayard during the 1870-80s, which ended only with the surrender of the Apache Chief Geronimo.

The first known interment at Fort Bayard was Sergeant David H. Boyd of the 3rd U.S. Cavalry, buried Oct. 10, 1866. In 1899, the Army deactivated Fort Bayard and established it as a tuberculosis hospital and research center. In 1922, the hospital was transferred to the Veterans Bureau, which became part of the new Veterans Administration in 1930. Fort Bayard Cemetery was established the same year, and became part of the National Cemetery System in 1973 when its administration was transferred from the Department of the Army to the Veterans Administration. In the 1990s, the state of New Mexico donated 3.95 acres to the cemetery.

Fort Bayard National Cemetery was placed on the National Register of Historic Places on July 7, 2002.

One of the most important civilians buried at Fort Bayard is Walter Foote Sellers, author of the poem, "The Kneeling Nun". He was the stepson of retired Brigadier General Walter I. Duggan. On his headstone is engraved "Ah, Me, the World Seems Lonelier Today."

In the civilian section of the cemetery near the fence on the east side is also buried John William Richmond Kennedy, who died at St. Joseph's sanitarium, Silver City, New Mexico on March 14, 1914. He was the eldest son of the Honorable William Rann Kennedy, Knt. P.C. of England.

The first burial at the Post cemetery with positive identification was Sergeant David H. Boyd, Company M, 3rd U. S. Cavalry, Oct. 10, 1866. One other, who is recorded as an "Unknown," preceded it.

New Mexico native Thomas P. Foy (1914-2011) graduated from the University of Notre Dame (IN) in the late 1930s and began to practice law. He enlisted in the National Guard in 1941 and went to the Philippine Islands. First Lieutenant Foy was in the Pacific that December when the Japanese attack on Pearl Harbor brought the United States into World War II. He was captured in April 1942 and was among the more than 70,000 Filipino and U.S. troops marched 60 miles across the Bataan Peninsula. Foy survived 44 months in a POW camp before being rescued; he received the Purple Heart, Bronze Star, and other commendations for his service. As a civilian Foy married and returned to his legal career. He was elected as county district attorney in 1949-1956 and to the state legislature in 1970-1998. Foy died October 6 and is buried in Section F, Row R, Site 15.