Fort Bayard was established as a United States Army installation in 1866 to protect miners and other settlers in the area along the Apache Trail.

The fort was named after Brigadier General George Dashiell Bayard, who was mortally wounded at the Battle of Fredericksburg in 1862.

Fifteen square miles of land were set aside as the Fort Bayard Military Reservation by presidential order in 1869.

Corporal Clinton Greaves, stationed at Fort Bayard with C Company, 9th Cavalry Regiment, received the Medal of Honor for his actions against Apache raiders on January 24, 1877.

A federal investigation of Fort Bayard Medical Center in 2006 found significant human rights violations.