Fort Gibson was established in 1833, on a plot of land within the Cherokee nation. It is at what is considered to be the end of the Trail of Tears. Frontier life was hard, yellow fever was common, and at least three separate cemeteries were created between 1833 and 1857 when the Fort was abandoned.
In 1863 the Fort was remanned by Brigadier General James G. Blunt. In 1868 the National Cemetery was established in a 7-acre (28,000 m2) plot, and all of the nearby cemeteries had their interments transferred to it. This included the remains of many civilians.
Fort Gibson National Cemetery was placed on the National Register of Historic Places on May 20, 1999.